Tuesday, October 09, 2012

What Is Evolution?

Most non-scientists seem to be quite confused about precise definitions of biological evolution. Part of the confusion is because the word "evolution" has many different meanings, depending on the context. When we talk about biology we are thinking about biological evolution and that's the term I want to define here. What do biologists mean when they refer to biological evolution?

This is a slightly modified version of a post from January, 2007 which, in turn, is a moified version of an essay that appears here. An even earlier version is on the TalkOrigins Archive.One of the most respected evolutionary biologists has defined biological evolution as follows:
Biological (or organic) evolution is change in the properties of populations of organisms ..., over the course of generations. The development, or ontogeny, of an individual organism is not considered evolution: individual organisms do not evolve. The changes in populations that are considered evolutionary are those that are ‘heritable' via the genetic material from one generation to the next. Biological evolution may be slight or substantial; it embraces everything from slight changes in the proportions of different forms of a gene within a population, such as the alleles that determine the different human blood types, to the alterations that led from the earliest organisms to dinosaurs, bees, snapdragons, and humans.
Douglas J. Futuyma (1998) Evolutionary Biology 3rd ed., Sinauer Associates Inc. Sunderland MA p.4
Note that biological evolution refers to populations and not to individuals. In other words, populations evolve but individuals do not. This is a very important point. It distinguishes biological evolution from other forms of evolution in science (e.g., stellar evolution). Another important point is that the changes must be genetic, or heritable—they must be passed on to the next generation. Evolution is the process by which this occurs and it is spread out over many generations. Thus, the short minimal definition of biological evolution is,
Evolution is a process that results in heritable changes in a population spread over many generations.
This is a good working, scientific, definition of evolution; one that can be used to distinguish between evolution and similar changes that are not evolution. Another common short definition of evolution can be found in many textbooks:
In fact, evolution can be precisely defined as any change in the frequency of alleles within a gene pool from one generation to the next.
Helena Curtis and N. Sue Barnes, Biology, 5th ed. 1989 Worth Publishers, p.974
... it's important to appreciate that natural selection isn't the only process of evolutionary change. Most biologists define evolution as a change in the proportion of alleles (different form of a gene) in a population.

Jerry Coyne in Why Evolution Is True (page 122)
One can quibble about the accuracy of such a definition, but it also conveys the essence of what evolution really is. When biologists say they have observed evolution, they mean that they have detected a change in the frequency of genetic variants (alleles) in a population. (Often the genetic change is inferred from phenotypic changes.) When biologists say that humans and chimps have evolved from a common ancestor, they mean there have been successive heritable changes in the two separated populations since they became isolated.

Unfortunately, outside of the scientific community, the common definitions of evolution are quite different. For example, in the Oxford Concise Science Dictionary we find the following definition:
evolution: The gradual process by which the present diversity of plant and animal life arose from the earliest and most primitive organisms, which is believed to have been continuing for the past 3000 million years
This is inexcusable for a dictionary that's supposed to be a dictionary of science. Not only does this definition exclude prokaryotes, protozoa, and fungi, but it specifically includes a term "gradual process" that should not be part of the definition. More importantly the definition seems to refer more to the history of evolution than to evolution itself. Using this definition it is possible to debate whether evolution is still occurring, but the definition provides no easy way of distinguishing evolution from other processes. For example, is the increase in height among Europeans over the past several hundred years an example of evolution? Are the color changes in peppered moth populations examples of evolution? Does the fixation of specific blood type alleles in some human populations count? The definition of evolution in the Oxford Concise Science Dictionary is not a proper scientific definition of evolution.
Standard dictionaries are even worse.
evolution: ...the doctrine according to which higher forms of life have gradually arisen out of lower.. (Chambers)
evolution: ...the development of a species, organism, or organ from its original or primitive state to its present or specialized state; phylogeny or ontogeny (Webster's)
These definitions are simply wrong. The problem is that it's common for non-scientists to enter into a discussion about evolution with such a definition in mind. This often leads to fruitless debate since the experts are thinking about evolution from a different perspective. When someone claims they don't believe in evolution they cannot be referring to an acceptable scientific definition of biological evolution because that would be denying something that is easy to prove. It would be like saying they don't believe in gravity!

Anti-evolutionists often claim scientists are being dishonest when they talk about evolution. The anti-evolutionists believe that evolution is being misrepresented to the public. The real problem is that the public in general, and anti-evolutionists in particular, do not understand what evolution is all about. Their definition of evolution is very different from the common scientific definition and, as a consequence, they are unable to understand what evolutionary biology really means. Scientist are not trying to confuse the general public by using a rigorous definition of evolution. Quite the contrary, saying that evolution is simply "a process that results in heritable changes in a population spread over many generations" is a way of simplifying discussions about evolution.

Note that I have described the minimal scientific definition of biological evolution. Nobody believes that this is all there is to evolution. There are other processes, such as speciation for example, that are clearly important parts of the process of evolution. [Macroevolution]

Objections to the Minimal Definition


Evolution consists of changes in the heritable traits of a population of organisms as successive generations replace one another. It is a population of organisms that evolve, not individual organisms.

"Science, Evolution, and Creationism" National Academy of Sciences (2008)
Some people, including some scientists, are uncomfortable with this minimal definition because they think it excludes some important parts of evolutionary biology. I'll try and discuss the various objections in a short while but first let me explain why we need a strict minimal definition in the first place.

I've already alluded to one of the classic questions that a proper definition can answer—the increased height of Europeans over the past five centuries. Armed with a good definition of biological evolution we can focus on one of the key requirements; namely, heritable change. It turns out that the increase in height is probably due to a better diet and not to genetic changes. Therefore, this is not evolution according to the scientific definition.

What about blood type alleles? Some populations of native Americans are homozygous for the O-type blood allele. Since this is a genetic change in a population over time, it is evolution, by definition. In this case, it qualifies as evolution even though it's likely that natural selection is not the mechanism.

We can also ask whether the development of antibiotic resistance in bacteria is a valid example of biological evolution. In this case the answer is "yes" because a new antibiotic resistance allele has arisen by mutation and subsequently became fixed in the population. Anyone who wants to offer an alternative minimal definition of evolution will have to make sure that it will help answer questions such as these.
Biological evolution, simply put, is descent with modification. This definition encompasses small-scale evolution (changes in gene frequency in a population from one generation to the next) and large-scale evolution (the descent of different species from a common ancestor over many generations).

Evolution 101
University of California, Berkeley

Sometimes it's convenient to refer to evolution as "descent with modification." This conveys a different impression of evolution than the minimal definition. Descent with modification refers to the long-term consequences of short-term changes within a population. It incorporates additional concepts such as speciation, which is an important part of macroevolution. Paleontologists are one group of scientists who aren't directly concerned with the minimal definition of evolution since they are mostly interested in the history of life. They have to deduce that evolution, in the sense of the minimal definition, has taken place from evidence of phenotypic change in the fossil record.

The bad thing about "descent with modification" is that it's not a very rigorous definition. It doesn't rule out modifications that are not genetic in origin and it doesn't rule out individuals evolving—as opposed to populations.

Many people are confused about the difference between a definition and an explanation. That's why we often see incorrect "definitions" that describe how natural selection works. This is wrong. In order to be useful, a definition has to enable us to distinguish examples of evolution from non-evolution but the definition should be neutral with respect to how evolution occurs. It should not distinguish, for example, between Lamarckian evolution and Darwinian evolution even though we know that one of these explanations is incorrect.

Attempts to define evolution in terms of natural selection are not only logically flawed but scientifically flawed as well. They exclude change due to random genetic drift when every evolutionary biologist agrees that drift is a mechanism of evolution.

Evolving Definitions

In 1997 a group of twenty scientists chaired by Douglas J. Futuyma issued a working draft of a "white paper" on Evolution, Science, and Society. The paper was written on behalf of eight scientific societies who wanted to make a statement about evolution. The initial draft defined evolution as,
Biological (or organic) evolution consists of change (modification) in the hereditary characteristics of groups of organisms over the course of generations. Such groups of organisms, termed populations or species, are formed by division of ancestral populations or species, and the descendant groups then change independently. Hence, in a long-term perspective, evolution is the descent, with modification, of different lineages from common ancestors.
This is a pretty good definition. It includes the minimal definition but adds the idea that long-term evolution is descent with modification. The initial draft definition was modified [final draft] so that on the current website it now reads,
Biological evolution consists of change in the hereditary characteristics of groups of organisms over the course of generations. From long-term perspective, evolution is the descent with modification of different lineages from common ancestors. From a short-term perspective, evolution is the ongoing adaptation of organisms to environmental challenges and changes.
This last sentence is really unfortunate. These twenty scientists have now agreed to a definition that specifically mentions the mechanism of adaptation. This is not how one should define evolution. One wonders whether they mean to exclude random genetic drift or whether they simply lost sight of their goal in trying to work out a compromise definition.

The Gene Centrist Objection


Evolution is the change in the inherited characteristics of biological populations over successive generations.

Wikipedia
Ernst Mayr wrote an entire book on the subject of this little essay. One might expect some insight from one of the original founders of the Modern Synthesis but, unfortunately, we aren't going to get any help from Mayr. On page 157 he says,
Evolution in sexually reproducing organisms consists of genetic changes from generation to generation in populations, from the smallest local deme to the aggregate of interbreeding populations in a biological species.
Ernst Mayr (2001) What Evolution Is, Basic Books, New York p.157
This is good stuff. It restricts the changes to genetic changes and it clearly identifies the population as the unit that evolves. There's no mention of any particular mechanism. But—and you knew there was going to be a "but" didn't you?—good things never last. In his chapter on macroevolution Mayr describes the work of his colleagues Rensch and Simpson. These workers were able to study macroevolutionary events without referring to allele frequencies in a population. Mayr coments,
This approach was consistent with the modern definition of evolution as a change in adaptedness and diversity, rather than a change in gene frequencies, as suggested by the reductionists.
Ernst Mayr (2001) What Evolution Is, Basic Books, New York p.189
Consistency is not one of the hallmarks of Ernst Mayr's writings. That's why he can propose two conflicting definitions in the same book; even a book that's devoted to the topic of defining biological evolution! Nevertheless, Mayr does highlight two different objections to the minimal definition that I am defending.

First, Mayr wants a definition that restricts evolution to the mechanism of adaptation. This is a lost battle. There may have been at time in the 20th century when a majority of biologists rejected random genetic drift and other non-adaptationist forms of evolution but that time is long gone. Mayr was one of the last hold-outs. Besides, as I mentioned above, it isn't appropriate to restrict the definition of evolution to a particular mechanism even if you strongly believe that it's the only possible mechanism. That's not how you define something.

Second, Mayr doesn't like reducing evolution to the level of the gene. This charge of reductionism is more interesting. In spite of the fact that Mayr was one of the founders of the Modern Synthesis, he never had much respect for genes and population genetics, or "bean-bag genetics" as he called it. He makes this point very strongly in the preface to his book.
... most treatments of evolution are written in a reductionist manner in which all evolutionary phenomena are reduced to the level of the gene. An attempt is then made to explain the higher-level evolutionary process by "upward" reasoning. This approach invariably fails. Evolution deals with phenotypes of individuals, with populations, with species; it is not a "change in gene frequencies." The two most important units in evolution are the individual, the principle object of selection, and the population, the stage of diversifying evolution.
Ernst Mayr (2001) What Evolution Is, Basic Books, New York p.xiv
I happen to agree with some of those who criticize the extreme reductionist views of scientists like Richard Dawkins but in this case Mayr has it all wrong. When we define evolution as a change in the heritable characteristics of a population we are not reducing evolution to the level of the gene. We are merely stating that populations don't evolve unless they undergo genetic changes. This is not controversial in spite of Mayr's objection. He is confused about the difference between a definition of evolution and a proposed mechanism of change—as was obvious in his attempt to include adaptation. This is a remarkable error in a book called "What Evolution Is."

The Minimal Definition and Macroevolution


The minimal definition of evolution is consistent with Hierarchical Theory and a focus on macroevolution as opposed to microevolution. This point is worth emphasizing since the minimal definition has often been criticized for excluding lots of evolution that takes place at higher levels. It's true that the minimal definition doesn't address the origin of populations (speciation) and it doesn't encompass potential higher level mechanisms such as species sorting, but that's not the purpose of a minimal definition.

Stephen Jay Gould—no fan of reductionism and no stranger to hierarchical theory—addressed this problem in his last anthology.
The Darwinian principle of natural selection yields temporal change—"evolution" in the biological definition—by a twofold process of generating copious and undirected variation within a population, and then passing only a biased (selected) portion of this variation to the next generation. In this manner, the variation within a population at any moment can be converted into differences in mean values (such as average size or average braininess) among successive populations through time.
Gould, S.J. (2002) "What Does the Dreaded 'E' Word Mean Anyway?" in I HAVE LANDED Harmony Books, New York p. 246
The purpose of his essay is to point out the fundamental difference between this biological definition and the common vernacular meaning of the word "evolution." (I wish he hadn't restricted his definition to natural selection—Gould knows that there are other mechanisms.) Gould points out that other sciences, such as astronomy, use the word "evolution" in a very different sense—one that is actually closer to the original nineteenth century meaning. The vernacular meaning carries an implication of purpose and direction that is entirely absent from the biological definition of changes in the heritable characteristics of a population over time. This is why Darwin never used the dreaded "E" word.

Gould argues that an understanding of the true importance of the biological definition is absolutely essential to understanding why the general public is confused. He is especially concerned about emphasizing the lack of progress and direction in the definition of biological evolution. He advocates that scientists owe it to the general public to teach the biological definition.
I don't mention these differences to lament, or complain, or to criticize astronomical usage. After all, their concept of 'evolution' remains more faithful to etymology and the original English definition; whereas our Darwinian reconstruction has virtually reversed the original meaning. In this case, since neither side will or should give up its understanding of "evolution"—astronomers because they have retained an original and etymologically correct meaning, evolutionists because their redefinition expresses the very heart of their central and revolutionary concept of life's history—our best solution lies simply in exposing and understanding the legitimate differences, and in explaining the good reasons behind the disparity of use.

In this way, at least, we may avoid confusion and the special frustration generated when prolonged wrangles arise from mis-understandings about words, rather than genuine disputes about things and causes in nature. Evolutionary biologists must remain especially sensitive to this issue, because we still face considerable opposition, based on conventional hopes and fears, to our emphasis on an unpredictable history of life evolving in no inherently determined direction. Since astronomical 'evolution' upholds both contrary positions—predictability and directionality—evolutionary biologists need to emphasize their own distinctive meaning, especially since the general public feels much more comfortable with the astronomical sense—and will therefore impose this more congenial definition upon the history of life if we do not clearly explain the logic, the evidence, and the sheer fascination of our challenging conclusion.
(ibid p. 250-252)
I agree with Gould. That's why I think it's important to explain the real biological definition of evolution as a change in the heritable characteristics of a population over time. We can explain that this is a minimal definition, and that there's more to evolution than this, but we shouldn't back away from the real meaning of the term since it conveys some important messages. If we cave to pressure from the general public to make evolution into something they can understand, with all their biases, then we will have lost the battle before we even begin.

The amazing thing about the minimal definition of biological evolution is that it doesn't carry any baggage concerning the history of life or its future. As soon as we try to define evolution in terms of the historical record, we run into all kinds of problems because we confuse evolution as a process with evolution as a history of life. The scientific definition attempts to describe the minimum thing that might be called evolution. We know that the history of life is more complicated than this and we know that evolutionary theory encompasses other things such as the formation and extinction of populations. There is no conflict between the minimal definition of evolution as a change in the genetic composition of populations and macroevolution. Gould understands this.


111 comments :

  1. This is a good working, scientific, definition of evolution; one that can be used to distinguish between evolution and similar changes that are not evolution.

    What I find attractive about your definition is that it also works for non-biological replicators. I'm a linguist, specialising in historical linguistics and theories od language change. I suppose you can guess why I'm interested in insights borrowed from biologists.

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    1. That's very interesting. I frequently use languages to illustrate divergence in biological molecular sequences, or as metaphors for better understanding evolutionary change. Neutral, semi-neutral mutations ...

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    2. I frequently use languages to illustrate divergence in biological molecular sequences

      It works both ways. I use biological concepts to illustrate various aspects of language change. Fortunately I haven't yet found any creationists among my students.

      or as metaphors...

      I would call them "analogues", since the underlying processes are "of the same kind" at a sufficiently high level of abstraction. In either domain, it's replication plus heritable innovation plus various mechanisms of fixation in a population. See Maynard-Smith and Szathmáry 1997 (The Major Transitions in Evolution), which has had a lot on impact on some linguists.

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  2. I'm YEC.
    Evolution is simply the claim that created biological entities, existing now or in the past, came to be from errors in reproduction but it actually made things survive quite well.

    Evolution is a rejection that biological entities were created by a thinking being.
    A rejection that biology is moving by laws, as in physics,
    A rejection that such wonderful complexity of moving parts is in fact complex.

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    1. In most cases two not necessarily thinking beings are necessary for the creation of new biological entities and the involved inheritance processes follow the well established Mendelian laws. In addition, most single beings reproducing alone are unlikely thinking much either.

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    2. Robert Byers:
      Did you read any part of the article?

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    3. A rather large portion of believers don't seem to see how accepting evolution means that living things couldn't have been created by a god. They generally have a lot more vague and abstract idea of what a god is and how it influences reality that you seem to though.

      As for laws, 'like in physics,' you've got to be willfully ignorant to think that we're saying biology ignores those. Random mutations are not random at the scale of particles, and even at the scale of chromosomes they're a biased random at best. You should know about this. It is the same random as when you roll a dice: not really random at all. You just can't keep track of small enough details to work out the result.

      Complex? Who in their right minds ever said life wasn't? Last I cracked open a bible it said that living things were made out of breath and dirt. Who exactly is saying life isn't complex again?

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  3. This is a very good essay. I just have two minor gripes.

    The second and third quotes from Ernst Mayr have changed his name to 'Mary'. I also don't think it fair to categorise Richard Dawkins as an extreme reductionist, and a little dig like this detracts from the essay as a whole.

    From what I've read, Dawkins' description of evolution is perfectly compatible with that as described by Jerry Coyne, Douglas Futuyama, Carl Zimmer and others. I've often thought that any difference of opinion is largely a matter of perspective: a molecular biologist looking at evolution sees mostly random changes in the genes, while an ethologist sees changes in animals and their behaviour which are clearly adaptive.

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    1. The second and third quotes from Ernst Mayr have changed his name to 'Mary'.

      Thanks, I fixed that.

      I looked hard for a definition of evolution in all of Dawkins' books and essays but I couldn't find one. In most cases he used "evolution" and "natural selection" as synonyms but I know for a fact that he's aware of random genetic drift.

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    2. While Dawkins may not define evolution in sound-byte terms, his chapter "the replicators" in The Selfish Gene is essentially a lengthy depiction of the core of descent with modification, with the emphasis firmly on the centrality of the genetic component - the stuff of inheritance - with changing phenotype being the outward medium through which this genetic 'competition' is scored (even effectively-neutral genes 'compete' in finite populations - it's just that none has an edge).

      He is much more interested in non-neutral evolution, for sure. But I too think he is unfairly criticised for 'ultra-reductionism'. Though he uses the term 'gene' in his attention-grabbing title, he makes it clear on many occasions that his 'gene' is simply any length of DNA, delimited, in the case of sexual species, not by product boundaries but by rather fuzzy recombinational ones. And it seems reasonable to me to make that recombinational, subgenome competition the baseline in such species, granted that effects at other levels integrate to make the whole - evolution on the grand scale.

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  4. Hey,

    just wanted to move at a tangent to this and ask about views on increasing genetic complexity over the evolutionary timecourse. There is a lot of talk about natural selection as a driver in this process (generally, especially in the public domain) - of course the biggest issue is not how organisms adapt and change over time, the biggest question is where did the genes come from in the first place..

    Now, laying aside the astronomically long odds of generating something which looks like an NTP (in puddle water), and those NTPs joining together in a sensible pattern to create a molecule which can replicate itself completely and accurately (no known examples to my knowledge), how do you then get from a situation where transcriptional fidelity is not important? To diverge genes you need a lot of mutation...which doesn't seem consistent (to my mind - I am open to explanations) with the process required to end up with intelligible genetic material.

    I could go on, and in much more detail, but I'll wait to see if anyone wants to chat.

    Thanks,
    Jonny

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    1. I don't think NS drives towards complexity in the general case. What appears to happen is that evolution bodges. Rather than keeping to an economic 'baseline', new genes add a layer to an existing set, to which other genes add other layers, which changes the game ... it doesn't fundamentally matter whether the change is beneficial (NS) or neutral. If detrimental, NS will tend to weed it out, leaving the rest, of which the beneficial fraction has the best odds of persisting.

      In certain species (prokaryotes, particularly), there are mechanistic limits on complexification. There are many things about the prokaryote lifestyle that keep it comparatively simple - cell walls, an external energetic membrane, diffusion of metabolites rather than engulfment, single origins of DNA replication, close competition with neighbours ... these things kept prokaryotes as the only game in town for a couple of billion years (and they've done OK since).

      For my money, several things mark out eukaryotes are complexifiers par excellence: mitochondria, sex, multiple origins of replication and a cytoskeleton. None of these, IMO, evolved for complexification, but each lifted the lid on constraints towards simplicity, allowing the evolutionary bodgers to survive and ultimately to explore niches undreamt of by our prokaryote cousins.

      As to the rest - warm little ponds and astronomical probability calculations on unknown events etc - it's simply a different issue. We don't know how replication arose. But we do know how replicators behave. It is true that unrestrained mutation is a killer for a proto-evolutionary scenario completely lacking in fidelity. But fundamentally, a replicator needs to generate 'daughter replicators', having the property if not the exact sequence of the parent, at an average rate in excess of 1, to ignite the spark.

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    2. Allan, thanks for the reply.

      Your first paragraph brings me to the issue of "neutral" additions. Can there be such a thing in a primordial soup scenario? An extreme (and unrealistic) example: 2 organisms, both with a single gene each – the replicator itself. Second organism somehow duplicates the gene, passing to next generation. Second organism F1 now has twice the transcriptional burden for no selective advantage, relative to the F1 of the first organism. Even the concept of increasing genetic complexity in an early life scenario doesn't really make sense - in an environment which would have seen FIERCE competition for resources.

      Nice to hear somebody actually say that "we don't know" for a change...

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    3. Allan Miller says: I don't think NS drives towards complexity in the general case.

      I think NS drives towards ‘all directions’, depending upon the environment.

      Take for example, viruses. You don’t hear much about viruses at Sandwalk, but:

      (i) viruses are the most abundant biological entities on our planet,

      (ii) their genetic repertoire surpasses that of cellular species, and

      (iii) viruses are highly significant for public health (e.g. viruses have killed hundreds of millions of people), environment (e.g. viruses have a leading role in global carbon and nutrients turnover by killing approximately one third of all bacteria on our planet every day), and genome evolution (e.g. the number of endogenous viral sequences in animals and plants dwarfs those of their hosts).

      So one of the biggest, if not the biggest unresolved issue in biology is the origin and evolution of viruses.

      Fortunately, there are only two broad ways of thinking about the evolution of viruses: they evolved from simple to complex by increasing the size of their genome, or from complex to simple by reducing the size of their genome. This evolutionary pathway is key evidence for their origin.

      The current prevalent hypothesis is that viruses originated from some mysterious simple genetic elements before the origin of cells, and that they evolved by acquiring new genetic material into complex viruses such as poxviruses, chloroviruses, or mimiviruses whose genome is several times larger than the genome of many cellular organisms.

      Alternately, I proposed that ancestral viral lineages originated from parasitic or endosymbiotic cellular organisms that fused with their host cells, and that these ancestral viruses evolved by reductive evolution, that is by losing genetic material, into a myriad of viruses with diverse complexity, genome size, and life cycles ( http://precedings.nature.com/documents/3886/version/1).

      So, which of these models is more likely to be correct? I think that the current data and observations are more consistent with the fusion model and with the reductive evolution of viruses.

      However, there is a more compelling reasoning based on common sense. As you know, in addition to viruses, there are thousands of intracellular parasitic or endosymbiotic bacterial, archaeal, and eukaryal species. Although, these organisms do acquire occasionally some new genetic material, there is overwhelming evidence that, overall, they have evolved by reductive evolution from more complex ancestors. Basically, this is considered a ‘fact,’ and it fully accepted by all researchers in the field!

      So my common sense question is this: if all parasitic or symbiotic cellular species have evolved by reductive evolution, why would parasitic or symbiotic viral lineages evolve any other way?

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    4. viruses have a leading role in global carbon and nutrients turnover by killing approximately one third of all bacteria on our planet every day

      Amazing. The average doubling time of bacteria is about 5-7 days in marine environments so it's a wonder that there are any bacteria left.

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    5. Jonny Dalzell says,

      Now, laying aside the astronomically long odds of generating something which looks like an NTP (in puddle water), and those NTPs joining together in a sensible pattern to create a molecule which can replicate itself completely and accurately (no known examples to my knowledge), ...

      I think that the "Primordial Soup" scenario is really, really, stupid. I much prefer "Metabolism First," in part because it avoids the very problem you raise.

      See: NASA Confusion About the Origin of Life: Part II and the links in that post.

      This doesn't mean we have the answer to the origin of life. It just means that we are eliminating some of the more fanciful ideas that have been around for decades.

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    6. Larry Moran says: Amazing. The average doubling time of bacteria is about 5-7 days in marine environments so it's a wonder that there are any bacteria left.

      Indeed, amazing!

      Some scholars in the field, such as Carl Zimmer, put this number even higher, when he says in his Book ‘Planet of Viruses”:

      “They invade a new microbe host ten trillion times a second, and every day they kill about half of all the bacteria in the world’s ocean” (emphasis mine)

      You might not have read Carl’s book, but he has been saying this in dozens of interviews and seminars such as in these:

      http://www.npr.org/2011/05/06/136057352/carl-zimmer-explores-the-weird-lives-of-viruses

      http://fora.tv/2011/06/07/Carl_Zimmer_A_Planet_of_Viruses

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    7. Larry Moran says: I think that the "Primordial Soup" scenario is really, really, stupid. I much prefer "Metabolism First," in part because it avoids the very problem you raise

      I think you can add to your ‘stupid list’ the ‘RNA world’ hypothesis. Like you, Larry, I prefer ‘Metabolism First’ (after all, we might have some ideas in common!).

      Well, my model on the origin of life adds a little bit of rationale and common sense to the ‘Metabolism First' idea, by saying that this ‘metabolism’ had to take place in ‘something,’ otherwise it will be all over the ocean, if you get my point.

      For a description of this model on the origin of life, which is all called a ‘cell-like world’ model on the origin of life on Earth you can take a look at this paper, entitled: A Unifying Scenario on the Origin and Evolution of Cellular and Viral Domains, which you can read for free at: http://precedings.nature.com/documents/3888/version/1

      This is a long paper, which might be difficult to read; so, you might want to focus on pages 7-11, which describes the model. If you have any questions please don’t hesitate to ask.

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    8. Claudiu Bandea seems to believe what Carl Zimmer wrote,

      “They invade a new microbe host ten trillion times a second, and every day they kill about half of all the bacteria in the world’s ocean” (emphasis mine)

      This is even more amazing than killing off one third of all bacteria every day. It means that, in order to survive, bacteria in the ocean have to double in numbers every day!

      Not even the intestinal bacteria in a well-fed person doubles as fast as that and those are ideal conditions.

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    9. Larry Moran says:
      Claudiu Bandea seems to believe what Carl Zimmer wrote,
      “They invade a new microbe host ten trillion times a second, and every day they kill about half of all the bacteria in the world’s ocean”


      Is not about me believing that Carl Zimmer wrote that! I have his book in front of my eyes and that’s what he wrote on page 43, first paragraph:

      “Marine viruses are so powerful because they are so infectious. They invade a new microbe host ten trillion times a second, and every day they kill about half of all the bacteria in the world’s ocean”

      Are you saying that Carl Zimmer is wrong?

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    10. Are you saying that Carl Zimmer is wrong?

      Duh! YES!

      (But please don't tell him I said that.)

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    11. Larry: Duh! YES! (But please don't tell him I said that))

      That’s a good one!! I’ve been already on the phone with my buddy Carl for over 2 hours; we have't finish out talk yet, but I think he begs to differ!

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    12. I think that the calculation was probably made taking into account the doubling rate of E coli (under ideal culture conditions), how quickly can some T-phage infect it, and so on ...

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    13. To use a subtitle from an article entitled “Viruses in the sea” by Curtis Suttle, published in Nature, “Accurate estimates of virus-mediated mortality are elusive” (http://www.ncbi.nlm.nih.gov/pubmed/16163346).

      My statement that viruses kill approximately one third of all bacteria every day is based on published estimates such as the one made in the same article by Curtis Suttle, a leading researcher in this field:

      “Nonetheless, accurate estimates of virus-mediated mortality remain elusive, and we are not much further ahead than a decade ago when viruses were estimated to kill 20–40% of marine bacteria on a daily basis”

      That said, I don’t know how Carl Zimmer derived his figure of 50%, although I have seen papers with that or even higher numbers. And the reason for that is that there are high temporal fluctuations in the number of hosts and viruses in both water and sediments.

      Also, I think that Carl wanted to emphasize the significant role of viruses in the ecosystem, so in this context it makes little difference if viruses kill half, or a quarter, of bacteria every day.

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    14. Also, I think that Carl wanted to emphasize the significant role of viruses in the ecosystem, so in this context it makes little difference if viruses kill half, or a quarter, of bacteria every day.

      Actually it makes a great deal of difference. No species could possibly survive if half of all individuals were killed every day. They couldn't survive if only one quarter of all individuals were killed per day.

      This is just common sense.

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    15. Now, you are saying that even your esteemed compatriot, Curtis Suttle, doesn’t know his science, which he help to established?

      Delete
  5. Also, using the term "IDiot" isn't very becoming of a learned individual, is it?

    It's a little embarrassing. If you claim to work according to rationality there is no need to lower yourself into schoolyard jibes. Show some respect to yourself, and others.

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    1. Someone named Jonny Dazell has a twitter account and he is identified as ...

      Saved and justified by Christ. Privileged to work with the youth at Straid Congregational Church. Research scientist by trade. Northern Ireland

      Is that you? What kind of research do you do?

      Are you unfamiliar with the rough and tumble of the evolution/creation war? If so, maybe you should stay out of the kitchen.

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    2. Yes, that's me. I work mostly on small RNAs, gene silencing. Just recently got a fellowship to develop new crop transgenics, and Gates Foundation grant to develop pathogen resistant staple foods for Africa.

      My point is that insults are an emotional response, not a rational one. I'm not looking for an argument - just pointing out that insulting people alienates people, and so conversations that may have occurred, may not occur at all.

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    3. As for me, I have no issue discussing with people who don't think or believe as I do. So there is no issue with the heat of the kitchen.

      Do you not think that this kind of emotional hostility damages efforts to disseminate scientific findings to certain quarters of the public?

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    4. Jonny Dalzell asks,

      Do you not think that this kind of emotional hostility damages efforts to disseminate scientific findings to certain quarters of the public?

      No.

      This fight isn't about rational discussion of science. If it were, the creationists would have lost 50 years ago. What we have is mostly a bunch of ignorant amateurs attacking evolution and science and telling their followers that scientists are stupid.

      You don't bring a sharp pencil to that kind of gunfight if you hope to survive.

      Many people tried the rational approach over the past century and it clearly didn't work. My goal is to expose the stupidity and nonsense that permeates creationist propaganda. You don't do that by just calmly explaining the correct science because nobody will listen to you.

      Similarly, you can't expose liars by just telling the truth. You actually have to make it known that they are lying. (You do know, don't you, that many of your creationist colleagues tell lies?)

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    5. I don't think that using abusive language and threats when talking with anyone, including scientists, is helpful!

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    6. I don't have any particular dog in this race, but I just expect people to be able to back up their words. That creationists go around telling people that 'scientists are stupid' seems a bit of a stretch to me.

      I wonder if Larry might be able to produce at least one example of this, where those or nearly those exact words are used, from a speech or a blog site?

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    7. Laurence,

      Again, I disagree, but I'll not push it.

      I just don't understand why you can't see the fact that you are practising faith here also. You can't tell me with any certainty how life started here on Earth. Sure, you can tell me what you think happened, and why, but you actually have no hard data on it, because it is temporally impossible to do so. As a scientist, as a rationalist, hard data is what you claim to work and live by - but there is clearly an inconsistency there. You base your worldview on backward conjecture from data collected today, from trends which we observe etc.

      There is a leap of faith there on your part - there is no point in denying that. To call other individuals "stupid" for placing their faith in a different direction is fairly condescending.

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    8. I'm also a little confused about your invoking a moral disagreement with regard to "lying" creationists? If morality is common to humanity, it is certainly independent of genotype. What issue do you have with truth or falsehood when it comes to biological life?

      If you believe that we are still subject to the laws of natural selection (which I guess that you do), then you have no business believing in, and judging on the basis of a moralistic criterion.

      Genes propagate themselves selfishly from one generation to the next with little regard for others...Lying must be the phenotype of a certain genotype, so I don't understand an atheist evolutionist disagreement with it.

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    9. Jonny, you may as well have gift-wrapped that one........

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    10. lol, how's that Andy?

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    11. PS. love your artwork.

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    12. Andy, I appreciate that the whole morality argument is regularly given the smack down, but only because I believe people are under-thinking with regard to how natural selection works - at the level of individual genes. If you have a moral system that bypasses the selective processes involved in natural selection, then the evolutionary worldview falls to pieces. Natural selection acts on genes, not populations. That is fact. Talk of eusocial animals is moot because they are often clonal - so it is really a gene thing, not a population thing.

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    13. If you have a moral system that bypasses the selective processes involved in natural selection, then the evolutionary worldview falls to pieces.

      You wish! If you have a 'gene for morality', or even some less simplistic concoction of multiple genes and social pressures, the remainder of evolutionary theory, on the rest of the genes that make the millions of individuals in the millions of species on earth is hardly likely to be troubled.

      And any sensible evolutionary approach to resolving assumed difficulties for 'naturalism' implied by the 'morality question' needs to have some idea about the selective coefficients and forces involved. I doubt that there are any data, either way.

      I don't think anybody invokes genetic forces for every last thing we think. Genes build brains, and they are afforded a certain latitude, which is why they are such a successful adaptation.

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    14. Jonny,

      why you can't see the fact that you are practising faith here also. You can't tell me with any certainty how life started here on Earth. Sure, you can tell me what you think happened, and why, but you actually have no hard data on it, because it is temporally impossible to do so

      What faith is that? Are you implying that not knowing how life started means that we should think that there is a god, and that if we don't accept such ludicrous idea then we are practising as much faith as a believer in gods? Truly? Do you really think that not knowing stuff makes gods any more real? So, should we accept the possibility of leprechauns too? After all, we do not know everything about how gold has gotten into those mines. What about flying spaghetti monsters as creators of life? Why not hyper-dimensional insects as creators of life? If you don't accept any of these then you are acting by the very same faith, right? That seems to be your logic. How much more nonsense do you reject by faith alone Jonny? It must be exhausting.

      The argument from morality? Seriously? Universal? You don't see the advantage to gregarious animals to be able to trust each other as something that natural selection would favour? You don't see that "morality" is not so universal other than in its most basic inclinations? (within group protection/sharing) You don't know of any humans who lack any sense of any such inclinations either? Moralities are very variable. They are the results of both, some natural inclinations, and then lots of cultural histories and developments. Take a look at reality for once.

      Yeah, you might as well have wrapped that up as a demonstration that creationism leads people into the most ridiculous "logics" and arguments imaginable. I bet that now you will give further demonstrations of creationist nonsensical arguments. Guess what? I have heard them all. None is convincing. All are rhetorical bullshit. So be my guest displaying some more creationist stupidity. (Ridicule is all these arguments deserve. I add a bit of explanation because then you can't complain of not having answers, and because some readers might benefit from them. I doubt that you will get anything though.)

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    15. Oh shit Jonny, you are an incredibly huge ass-hole.

      Objects attract each other by gravitation...Falling off a precipice must be the natural consequence of objects attracting each other, so I don't understand an atheist gravitationist disagreement with tossing people off them.

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    16. ... because you know, understanding natural processes means that we should worship them
      ... (what an ass.)
      ... ("laws" of natural selection! pendejo, pendejo, pendejo, pendejo ...)

      I rather go, I can only withstand a limited amount of such levels of imbecility. And he acts surprised that we "insult" creationists! (?) Oh shit, oh shit!

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    17. @ Jonny 'lol, how's that?'

      First of all, thank you for taking a look at my blog(s)! I am glad you found things there that you enjoyed.

      The reason I have such distaste for your comment, and think it merits a thorough smack down, is due to the nature of your purpose in making it. Obviously, you do not wish for, nor do you have any expectation that, Larry will read it and reply, "Jonny! You are right! What was I thinking all this time? From now on I am going to tell lies all the time and furthermore will hold it against no other person should they do the same! In fact, I may just go about praising them for doing so!"
      Since you are not trying to get a person to abandon a moral position that they already have, and that you presumably share, your only purpose seems to be to score a point.

      I find this to be a false, fruitless form of 'debate'. A lesser form. As you well know, in discussions of this nature, points are rarely conceded, and even the attempt to get people to see things from a different perspective is generally unsuccessful. Therefore I think it wastes everyone's time to try to score a point that a) has basically zero potential of shifting anyone's views, and b) would result in something negative happening even in the unlikely event that it did manage to persuade.

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    18. Negative Entropy,

      You said "You don't see the advantage to gregarious animals to be able to trust each other as something that natural selection would favour?"

      No, I don't. Natural selection works on a gene by gene basis, not on a population basis. If you had (for arguments sake) a gene which encoded a protein which functioned in some kind of internal moral calculator, which made decisions on anything other than the competitive advantage on gene allele gives over another, then you remove a significant amount of selective pressure off those genes. I agree, it is difficult to tell to what degree that easing of pressure would be. However, given that NS is a gene issue, I believe that any such mechanism would be selected against because of the jealous propagative nature of each individual gene. Also, how would a genetic basis for morality survive the wild? One mutation leads to a function of reduced aggression to neighbouring families / prides / clans etc? That family / pride / clan starts encroaching on your territory, you lose resources...it spirals logically downward from there.

      @andyboerger,

      I understand your view, you may be surprised to hear that I share them. In my defence, I did not view that as a "point scoring" attempt, that was a legitimate attempt to make a specific point which was pertinent to the discussion - mainly that there are other considerations, and WRT my earlier conjecture of requiring "faith" to stand by an evolutionary worldview. By the way, I stand by that.

      I WAS NOT suggesting anything other than to get to a confidence in an evolutionary worldview means that you MUST by definition be displaying faith in the unknowns being one day known. That is an entirely logical, and true statement. I wasn't suggesting as Negative Entropy bizarrely does that I expect that faith to lead to worship. I place my faith in a different direction which does require worship. I merely state, that all this talk of rational attitude to available data is really nonsense when people so aggressively defend a position that they can't in face substantiate with actual data. Thats it.

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    19. A quick idea here for you: what if morality isn't some cripplingly stupid behavior that should doom your genes, but rather something that is actually effective and generally useful for social species?

      Take deer for example: while the males compete for mates they don't take "dirty blows" if one of them stumbles or slips and falls for a moment. Although they would have a good chance at killing the competitor during such a slip up there is also the cost of failure to take into account. If they fail to seriously injure them at this time then they have gone from a situation where they would probably just have injured pride if they lost, into one where the opponent is perhaps furious enough to kill them given the chance.

      On a purely rational basis it makes sense for us humans to not murder the people around us, as the future is too volatile for us to know and as such we may very well be reliant on those people for survival. It may not be an especially likely event but the paltry cost of making friends instead of bitter enemies has an obviously enormous benefit for us if we do find ourselves in situations where we and/or our children would starve to death alone.

      Whether this works out as a net gain in the grand statistics of society is only obvious if your personal philosophy doesn't cloud the issue very much, but I can save you the trouble of looking into it by telling you that all signs point to yes.

      If you still can't see any survival benefit behind general morality then perhaps you could list some of the basic benefits you would gain by abandoning it?

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    20. "....as the future is too volatile for us to know and as such we may very well be reliant on those people for survival. It may not be an especially likely event but the paltry cost of making friends instead of bitter enemies has an obviously enormous benefit for us if we do find ourselves in situations where we and/or our children would starve to death alone. "

      and this would have been a much likelier event for most of our history when the population was so small, both overall and in terms of the sizes of the tribes people lived in when the trait was asserting itself in our species.

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    21. I WAS NOT suggesting anything other than to get to a confidence in an evolutionary worldview means that you MUST by definition be displaying faith in the unknowns being one day known. That is an entirely logical, and true statement.

      Sorry, but it's a silly statement, silly in several ways. First, there is no such think as an "evolutionary worldview". The acceptance of evolution (just like any other finding of science) is much easier if your worldview is generally rational, but it doesn't depend on any such "faith". Religious faith is based on the subjective feeling of certainty that your favourite god exists, no matter if his existence is rationally demonstrable. What you would like to call scientific faith is NOT a certainty but simply a generally optimistic attitude towards unknowns (a.k.a. curiosity). We REALISE that lots of current unknowns will likely remain unknowable forever, but we don't give up trying. This optimism is reasonable and justifiable, as demonstrated by the rate of scientific progress in the past three centuries or so. It is not limited to evolutionary biology but characterises science in general. That's why a rationalist faced with a mystery naturally tries to solve it rather than preserve it as a sanctuary of the Lord of Gaps.

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    22. "and this would have been a much likelier event for most of our history when the population was so small, both overall and in terms of the sizes of the tribes people lived in when the trait was asserting itself in our species."

      Of course there's our developmental past to think about but I'm doubting you can get agreement about that premise here, and the point I was making doesn't require it. Morals are a subset of social behaviors that still benefit us in a lot of ways today.

      You can easily say that the morals that aren't accepted (virtually) everywhere are probably not prerequisites of a society that can span at least a few centuries, but arguing about whether tradition or innovation ultimately serve humanity better is an argument that comes after you've got everyone admitting that there is a tangible benefit behind morality and social grouping in general.

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    23. Jonny,

      No, I don't. Natural selection works on a gene by gene basis, not on a population basis

      No ass-hole, natural selection acts on phenotypes. Genes are selected via the phenotypes that they confer. Genes allowing for trust within the tribe will be much more likely to survive in animals who require each other's help. The process, of course, is not perfect, and we can witness the imperfection (unless you have indoctrinated not to be able to understand that moralities are not universal). How much of an imbecile are you not to understand this? Oh, sorry, a lot, after all you subscribe to creationist rhetorical bullshit. (Shoku gave you a much more patient explanation, maybe you should take a look.)

      ... evolutionary worldview means that you MUST by definition be displaying faith in the unknowns being one day known

      What fucking "evolutionary worldview" are you talking about? Accepting a reality out of the evidence does not mean that you make such reality your "worldview." Do you have a "gravitational worldview" ass-hole? Do you instead accept the reality of gravitation? If you do (who knows, maybe not, you might be that much of an ass-hole), does it mean that you "MUST by definition be displaying faith in the unknowns being one day known."?

      I wasn't suggesting as Negative Entropy bizarrely does that I expect that faith to lead to worship

      Ironically you said this after suggesting worship, yet again, by describing evolution as a "worldview," rather than as a natural process. Yet, the "faith" part is not precisely the part I cited about worship (nice try at distracting from your original stupidity though). The part about worshipping comes when you call somebody an "evolutionist" and then imply that because something might have been the product of "natural selection" via genes then the "evolutionist" should have no problem with it. Just projecting evolution into that person's mind as your god is in yours. If your god said so, then you have to accept it. See ass-hole? It is you who exchanges your god for a natural process. Somebody who accepts that a natural process exists does not necessarily make the natural process into an object of worship though.

      when people so aggressively defend a position that they can't in face substantiate with actual data

      Do you really think that there's no data supporting the reality of evolution? Oh, sorry again, obviously you think that there's no data. After all, you subscribe to creationist rhetorical bullshit. Next, with that astounding non-sequitur nature of creationist bullshitters, you will say that if we don't know how life started evolution is false. Because, you know, the facts that we unquestionably share common ancestry with the rest of the apes, et cetera, et cetera, mean nothing if we can't solve the question about origin of life. Same goes for gravitation shaping the orbits of the planets. It is false unless we can solve the problem of the origin of the universe. Makes perfect sense!

      How ironic that you started by complaining about "insults" to creationists, only to then show these levels of stupidity. The levels are so bad, that when I write these adjectives I fell like I am complimenting you instead. Perhaps I should be apologizing to real idiots and ass-holes for comparing them with you.

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    24. Jonny,

      While I am extremely happy putting your "arguments" back into your ass, I suggest that you stop imagining that your training in creationist rhetoric might get you out of the diarrhea where you dived in when you started commenting. Reason carefully and critically about the creationist rhetorical crap that you have so far learned (I notice that you have added to it, which is kind of "creative," but does not make it any less stupid), and you might be able to get out of the diarrhea all by yourself.

      No need to thank me.

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    25. Although patient I would like to make it clear that I find it very insulting to be told that I 'must think' that inane drivel on the assumed basis that Jonny heard some public speaker say something vaguely similar that he thought was very convincing. I'm insulted that he thinks he all he has to do is vaguely recall some bit of rhetoric to invalidate my years of sweat, study, and stubborn perseverance that have gone into actually learning about living things.

      But at the same time I don't think he knows any better and hasn't had any of the people around him ever indicate that he should learn any better. I would definitely like him to know how much outrage I would be justified to feel and express here, but instead opted to give him a small reprieve from that knowing that he's walked into the lion's den here and other people will do a better job of expressing that particular point better than I would.

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    26. Jonny, speaking of populations, what is your opinion on why all human, animal, or plant populations (or individuals) don't have exactly the same susceptibility or immunity to diseases?

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  6. Jonny Dalzell,
    Allan, thanks for the reply.

    Your first paragraph brings me to the issue of "neutral" additions. Can there be such a thing in a primordial soup scenario? An extreme (and unrealistic) example [...]


    The principles of evolution derive from a competition between 'organisers' - however big or small, replicating molecules collect the material that enables them to replicate and create copies of that system with the same capacity. Life is a chain reaction, provided, as I say, that replication capacity generates replicating systems at a frequency > 1. So the constraints on bare replicating molecules - if such can exist - would be similar to those on prokaryotes. Adding material may prove costly, but if the addition enhances speed, resists decay or whatever, then the possibility of selective enhancement of the replicating capacity is there. But whatever happens - if they are all equally capable - one sequence will always come to dominate. Which is why the baseline - neutral drift - still produces evolution, provided there is mutation. There probably will be selection against non-adaptive extension, but its intensity depends upon local conditions - 'population' size, mixing, material availability and energetic cost. It's likely to be proportionally higher for short replicators, certainly, but prohibitively so? And one should not forget the potential power of recombination, even here. End-joining two replicators produces a longer unit which has already paid the cost of accumulation. It costs more per unit to replicate that, but it depends on the abilities of that merged unit vs the 'wild-type' as to whether economy wins out against it.

    And just to note that, although I know Larry is not a fan of 'soupy' scenarios, I don't think non-replicating chemistry has the capacity to explore very far at all. Replication is central, IMO, though perhaps not possible free-floating in solution. I think simple proton gradients may be a primary energy source, but away from them, I don't see how, without replication, 'bare' metabolism can get itself out of entropic holes, elaborate and resist attrition.

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    1. And rereading, it strikes me as potentially misleading to assume too many parallels between constraints on prokaryotes and those on much simpler replicators. Prokaryotes are highly evolved organisms, and in a population of them, there is an apparent constraint on 'unnecessary' complication, because you rapidly get swamped by the 'optimised' neighbourhood. But amongst hypothetical ultra-minimal replicators, it may be that the selective environment is less intense, because your competitors aren't all that great either. We'd need some early replicators to really get to grips with that one!

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    2. Sure, I accept the premise of your argument, I just can't envisage that past the replicator. Thanks for fleshing it out though. I do agree that replication is central to the entire argument, although admittedly I know much less about the metabolism first concept than nucleic acid first.

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    3. I also agree that replication is essential. The difference between primordial soup and metabolism first is that, in the old-fashioned scenario the building blocks for replication are there from the beginning, whereas in metabolism first they are built up gradually from inorganic precursors.

      Thus, in the primordial soup scenario it is possible to envisage a time when there were lots of RNA catalysts and few polypeptide catalysts. That's because, by some unstated magic, nucleotides came into existence from the very beginning.

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    4. Thus, in the primordial soup scenario it is possible to envisage a time when there were lots of RNA catalysts and few polypeptide catalysts. That's because, by some unstated magic, nucleotides came into existence from the very beginning.

      I think there's a bit of hidden magic either way. A few reasonable attempts have built up nucleotides from simpler precursors, though amino acids certainly seem much more readily formed. But in either case, you have a problem of condensing the subunits. Triphosphatised nucleotides carry the energy required for that condensation (though it obviously isn't spontaneous), while amino acids do not. Nucleotides also carry the basis of their own specification, through complementary pairing, whereas amino acids need some means of external specification.

      Peptides are certainly much more versatile, but I don't see that their consistent generation, in order to become involved in primitive biosynthesis pathways, is any less hand-wavy. Without it, they are just another ingredient in the soup, and - though this is pedantic - I think it overplays the chemistry to call that 'metabolism'.

      Once replication got started, whatever external role peptides may have had in prebiotic synthesis, we cannot assume an immediate internal role in replication as well. Replicators either have to continually replenish them from an external source, or learn how to make them themselves. My bet is the latter, and until that point, they were RNA organisms, even if they did not simply pop out of a convenient pack of Nucleotide Soup.

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    5. Allan Miller: Once replication got started, whatever external role peptides may have had in prebiotic synthesis, we cannot assume an immediate internal role in replication as well. Replicators either have to continually replenish them from an external source, or learn how to make them themselves. My bet is the latter, and until that point, they were RNA organisms, even if they did not simply pop out of a convenient pack of Nucleotide Soup.

      Alan, can you please explain this in more detail, with emphasis on what were the ‘replicators’ and how did they ‘replicate‘?

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    6. Alan, can you please explain this in more detail, with emphasis on what were the ‘replicators’ and how did they ‘replicate‘?

      I spy a trick question. Obviously, I don't know. But as far as biological evolution is concerned, replication is its essence, and the extra layers that replication brings to 'raw' chemistry have been extensively characterised.

      We are attempting to bridge the gap between a bare planet and LUCA. LUCA was a replicator, we can assume, since all her descendants are. If we follow her ancestors back, we follow through a potentially long line of DNA replicators with protein synthesis, but with characteristics less and less like those we see preserved in modern life. At some point, one of her replicative ancestors arose by non-replicative means.

      We know that LUCA was a nucleic-acid replicator, with protein as part of phenotype. I'm not aware of serious proposals that would put protein in a role other than as phenotype within a replicator, which I see as distinct from a 'metabolism-first' scenario of being involved in primitive 'bio'synthesis of molecules with more than a handful of carbon atoms. It is a reasonable hypothesis that the first replicators - the earliest of LUCA's ancestors possessed of replicative capability - did not have protein genomes. That would be a tricky beast to read, which is indeed why there is a 'central dogma' of biology.

      Still ... I'm not sure what you are getting at. Obviously not the 'level 1' interpretation of your seemingly innocent question, since I know that you know that I don't know what pre-LUCA replication categorically involved. But at some point, prior to LUCA but after planetary formation, definitive replication did indeed get started, with all that it entails, and IMO is highly unlikely to have included a genetic code on Day 1.

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    7. @ Allan

      I think that your ideas and discussion about potential participation and interactions of amino-acids and nucleotides during the early stages in the origin of life are superior to those associated with the RNA world hypothesis promoted in most textbooks of biochemistry, biology, and evolution written in the last two decades.

      As you know, according to the RNA world hypothesis, which was based on the findings that RNA molecules can serve both as carriers of genetic information and as enzymes, life on Earth started with self-replicating RNA molecules.

      However, very little is known about the early synthesis of the ribo-nucleotide monomers and the synthesis of the first RNA molecules, so the scenarios about the “RNA world” usually start with ready-made, self-replicating RNA molecules.

      However, a template-based RNA self-replication process is more complicated than it is usually perceived, because in addition to a relatively high concentration of ribo-nucleotide monomers, this process would require the synthesis of a complementary strand that either had to self-replicate or somehow get replicated by the parental strand or by the duplex, a process with extremely low probability. As emphasized by a few good chemist and biochemists, including Christian deDuve, self-replication of RNA “does not make chemical sense.”

      My question about the ‘replicators’ and how did they ‘replicate’ was intended to emphasize that it is not enough to just present a view such as the RNA world hypothesis, and say that’s the way life originated, but it needs to be explained how did it happen.

      You see, unlike papers and textbooks which are usually peer reviewed by people with similar ideas and perspectives, here in the Blogosphere, you can’t just advance hypotheses or ideas such as ‘RNA world’ without answering inconvenient questions.

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    8. Claudiu - I think I flagged up the speculative nature of my position reasonably - 'my bet'. My own speculations were in response to others. Opponents of the RNA world are quite reasonably concerned about the biochemical difficulties and the single-strand replication question, but their alternatives are, as I say, no less hand-wavy IMO.

      To invoke protein is to simply introduce a bunch of other unsolved questions - particularly: how was it specified? The very versatility of protein catalysts is a difficulty for a loose specification system, because function is so easily broken or changed.

      It's as useful to think backwards from LUCA than forward from an abiotic earth. IMO (another speculation) the ribosomal system arose originally to generate peptides for non-catalytic purposes - structure, perhaps, polyglycine sheets or some other monotonous peptide. Only when a mix of hydrophobic and hydrophilic acids arose was it possible to generate protein catalysts.

      So - a question back to you - what, if any, was the role and specification system of protein in organisms prior to the evolution of the DNA-RNA-ribosome system? How were consistently foldable peptides achieved? And prior to there being any replication at all - how were these catalytic peptides specified, and what drove peptide bond formation?

      The central logic of the 'replicator' hypothesis (not necessarily RNA) is compelling. A linked set of genes - covalently linked - can explore nearby phase space and tune its replicative capacity. It is that linked genetic core which - as Dawkins has been banging on for many years - is the unit for whom modifications are 'to the benefit of'. So if you have such a core making protein, that protein is a phenotype that the core must make repeatedly to assist the overall replicative process over successive replications. I don't think you can put protein in at the start of replication, even if it had a role in chemical evolution. Having it just kicking around ready to assist some replicative process on demand is no better than the nucleotides-came-from-elsewhere misdirection.

      I accept that abiotic peptides may have had a role in primitive biosynthesis. Whether they had a role in assembly of the 'first replicator', who knows? But I don't see any realistic mechanism for producing tightly specified proteins that can assist replication other than those produced by quite a sophisticated replicator.

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    9. andyboerger said:

      "I don't have any particular dog in this race, but I just expect people to be able to back up their words. That creationists go around telling people that 'scientists are stupid' seems a bit of a stretch to me."

      Oh. Come. On. Your first sentence is a blatant lie and it also exposes the different standard you have for yourself versus other people, and your second sentence is a dishonest game in which you're pretending to be unaware of what creationists say and/or do.

      "I wonder if Larry might be able to produce at least one example of this, where those or nearly those exact words are used, from a speech or a blog site?"

      You know damn well that creationists have been viciously and sanctimoniously bashing science and scientists and anyone else they feel like targeting for as long as there have been creationists, and many creationists have gone way beyond verbal condemnation. Do you really think that you're fooling anyone with your dishonest games?

      You asked for at least one example. Here's one for you:

      http://intelligentreasoning.blogspot.com/

      joe g is a muslim IDiot creationist. You can also find him as a regular on the site 'Uncommon Descent' and doing hit and runs on some other sites, like The Skeptical Zone (check the Guano section). At UD you'll also find plenty of other creationists bashing science and scientists. And then of course there's AIG, ENV, etc., etc., etc.

      Delete
    10. TWT, I did not ask Larry to put up a site to show that creationists bash scientists. I asked HIM, not you to show me where they use the word 'stupid'. You jumped in and provided me a site that I'm not going to scroll down on. If you can provide a quote that includes the word 'stupid' from your link, please do so.

      That creationists 'bash' scientists wouldn't surprise me. It is not like I am suggesting there aren't boorish, small minded people like you included among subgroups of proponents of either position.

      Delete
    11. As for accusing me of 'a blatant lie', prove it.

      You keep associating me with Christians, or some form of evolution denying orthodox religion simply because you are a paranoid fool.

      furthermore, you will note that if I was really trying to trap Larry rather than simply requesting to back up his statement, rather than asking once and, not receiving an answer, dropping the question - which I did, I would have

      continually hounded and pestered him for an answer, the way YOU do with your inane babble about unicorns, pasta monsters, and bananas.

      May Fifi Be With You

      btw, please note that you pasted your question below the wrong thread. I am copying and pasting two answers and reposting them here as one. oy.

      Delete
    12. TWT,

      I don't think that Andy is lying or dishonest. I am convinced that he is quite unaware of creationist tactics and such. He gives lots of undeserving people the benefit of the doubt (I think that makes him a most excellent human being). He has not commonly witnessed the harsh discussions we have with the authentic IDiots and creationists of the shitty caliber of, say, Jonny Dalzell above. This becomes very evident because of his comments all around. he truly believes and promotes some kind of fairness and stuff that cannot be explained except if you first think that Andy is normally way too far from these discussions.

      I understand TWT, that we too often find creationist bullshitters, and that might make us suspect people quite too soon. But andy has never betrayed my trusting him to be honest. Not once has he answered me with some stretch of rhetorical crap. Not once has he started a series of red-herrings after I explain something. We might have talked a bit past each other, but that seems to be because we are speaking of different things thinking that we are talking about the same thing, or some other honest way for misunderstanding or barriers to communication (mine or his, who knows). That's it.

      (Maybe you have noticed that I have no problems insulting, slightly, IDiots and snake-oil-salespeople, but that happens after I identify them as such ... well, no, I have insulted a few before they show any dishonest stupidity, so now I try and be more careful not to repeat those mistakes.)

      Delete
    13. NE, thank you. I am deeply appreciative. The high regard I have for you has increased. :)

      Delete
    14. andyboerger barfed:

      "TWT, I did not ask Larry to put up a site to show that creationists bash scientists. I asked HIM, not you to show me where they use the word 'stupid'. You jumped in and provided me a site that I'm not going to scroll down on. If you can provide a quote that includes the word 'stupid' from your link, please do so."

      How old are you, 12?

      Here, let me give you a lesson that you need badly. Take another look at what Larry said. Did you look? No? Then I'll make it easy for you. Here's what he said:

      What we have is mostly a bunch of ignorant amateurs attacking evolution and science and telling their followers that scientists are stupid. (my bold)

      Now, tell me if you see quote marks around the word stupid. Well?

      Do you actually think that Larry has to prove that ignorant amateurs specifically use the word stupid for his point to have merit? Does Larry have to provide exact quotes of every derogatory thing that ignorant amateurs have said against evolution, science, and scientists for you to get his point?

      There are lots of ways in which ignorant amateurs attack evolution and science and tell their followers that scientists are stupid, even if they don't use the word stupid. And do you actually believe that no ignorant amateur has ever specifically called a scientist stupid or specifically told their followers that scientists are stupid?

      You really like to stupidly nitpick things just so that you can argue for the sake of arguing. I guess that's all you can do when you have no substantial arguments.

      Why are you afraid to scroll down on joe's blog? Don't you want to see what he says to and about scientists? He goes way beyond the word stupid (in more ways than one).

      "You jumped in..."

      This isn't your site, and I don't see where Larry, me, or anyone else asked YOU anything before YOU jumped in.

      "I was really trying to trap Larry..."

      Maybe my guess at your age being 12 was too high.

      And didn't you say in another thread that you aren't going to respond to me anymore?

      Delete
    15. Allan says: It's as useful to think backwards from LUCA than forward from an abiotic earth.

      I think this is a great approach for building up a sensible model for the origin of life and the first organisms here on Earth. That’s the approach I used to develop the ‘cell-like world’ model for the origin of life, which I discussed in the paper A Unifying Scenario on the Origin and Evolution of Cellular and Viral Domains, which you can read for free at: http://precedings.nature.com/documents/3888/version/1.

      This model addresses the origin of coupled replication, transcription, and translation, which is the central issue in understanding the origin of life and its evolution leading to LUCA.

      Delete
  7. To All Members of Sandwalk:
    On his own blog's masthead, the whole truth writes, concerning ID:

    "The people promoting and supporting it are insane, narcissistic, hypocritical, dishonest religious-zealots who want to control the thoughts and actions of everyone on Earth."


    I am curious as to whether others, who post here regularly, agree with this assertion. I don't mean to offend anyone, even by asking, and apologize in advance if I have done so. My assumption, of course, is that no one does.

    ReplyDelete
    Replies
    1. And I was being nice when I wrote that. :)

      Hey andy, why don't you read everything on my site, and read hundreds of articles at UD (and all of the comments or what's left of them after all the deletions and bannings), and read everything at ENV and joey's blog, and read the bible and koran, and read everything the 'leaders' of the 'ID movement' have said, and read everything on the Panda's Thumb and ATBC, and read everything at The Sensuous Curmudgeon, and read everything (or at least a lot) on many of the other sites/blogs that deal with ID or challenges to it, and read the wedge document, and read everything at the following sites:

      http://kairosfocus.blogspot.com/

      http://www.angelfire.com/pro/kairosfocus/

      http://uk.groups.yahoo.com/group/caribbeankairos/

      http://www.angelfire.com/pro/kairosfocus/resources/Info_design_and_science.htm

      and be sure to follow any links you come across and also do your own searching for anything related to ID and what the IDiot-creationists have said, including under their various user names, and then try to convince me that what I said in the header on my site is wrong.

      Delete
  8. andyboerger said:

    "As for accusing me of 'a blatant lie', prove it."

    Okay. You said:

    "I don't have any particular dog in this race, but I just expect people to be able to back up their words."

    You do "have a particular dog in this race" or you wouldn't say or expect anything, and you have shown many times what your particular dog is. You're a creationist and are against the theory of evolution and any theory of the OOL unless they include whatever designer-creator-spirit-god you imagine. And you obviously expect a lot more than just people being able to back up their words. What exactly does "be able to back up" mean to you, and are your words subject to the same standard?

    "You keep associating me with Christians, or some form of evolution denying orthodox religion simply because you are a paranoid fool."

    Can you show where I associated you with "Christians, or some form of evolution denying orthodox religion"? You're going to have to show where I used all those exact words, right down to the capitalization of "Christians". After all, if you can expect exact words from Larry and/or others I can expect the same from you. How do you like having your own games thrown back at you?

    I certainly have called you a creationist because you've admitted that you are one and because it's obvious that you are. You'll probably come back with something about a creationist is different than someone who says that they believe in a creator. Don't bother.

    ReplyDelete
    Replies
    1. sigh, twt, why do you make things so easy? This is the last time I am going to waste my time 'communicating' with you, because you are a clown.

      HERE! - you silly, Fifi-riding, self righteous, unhinged person is where you associated me with 'Christianity' uh.......................YESTERDAY:

      "Hey, at least I'm not suggesting that you should be nailed to a cross, although you'd probably like it if I did because that would give you an even better excuse to pretend that you're the mythical character jesus. "

      You can fall back on the argument that you didn't use the exact words, but here's the thing, FIfi; the readers of this site are NOT stupid. When clear evidence is shown to them, they can follow it quite well. They will know darn well that I had a reason for using the words I did.

      As for catching me in a blatant lie, please define what I meant when I referred to 'this race'. Go back, read the comments that preceded mine, and you may be in for a surprise.

      Delete
    2. You're still missing my points and you're the one who's making it easy. I'm so glad that you said this:

      "You can fall back on the argument that you didn't use the exact words, but here's the thing, FIfi; the readers of this site are NOT stupid. When clear evidence is shown to them, they can follow it quite well. They will know darn well that I had a reason for using the words I did."

      Yes, the readers of this site (well, many of them anyway) are not stupid and they can follow the clear evidence and easily find (if they don't already know) that Larry darn well had a legitimate reason for using the words he did in the generalized comment he made that you're stupidly nitpicking.

      When someone says something you don't like you expect perfection and exact quotes from them to "back up" their comments, even when their comments are generalized and CLOSE ENOUGH, but you don't live up to the same perfection and expectation with your own words. You want and expect people to interpret your words in a reasonably generous manner but you're not willing to do the same with the words of others when their words point out the truth about the arrogant, condescending, know-it-all behavior of your IDiot-creationist fellows and heroes.

      Delete
    3. twt, that is just flat out bullshit.

      I explained very clearly above - specifically because I knew otherwise you would try to score a bullshit point off of it - why I chose to hold LM to the line, 'telling their followers that scientists are stupid".

      As I have already explained, I am not surprised to see that some of them behave as obnoxiously as you do, and therefore might call scientists deluded, deceitful, misguided, blind, etc. etc. But that is NOT the same as calling them stupid. I explained that earlier. Not because I think they are too 'good' to do that, but because I doubt that they are stupid enough to.

      As for my 'IDiot-creationist fellows and heroes', again, you are just making ridiculous, unfounded assertions from your own fevered imagination.

      Find a single quote of mine that leads you to think that. When you do, I will match it with at least three quotes of mine that blow your dumb assertion out of the water. Deal?

      by the way, twt, I would just like to ask. What are your exact credentials, please? What scientific field are you involved in professionally, and why don't you mention it on your own blog? Why so demure?

      As for me, because I don't hide behind an alias, anyone can see that I am not a scientist; I am an artist and writer.
      HOw about you? My guess is that your profession, like mine, has nothing to do with science. This based on your demeanor and the sloppy way you argue.

      MFBWY

      Delete
  9. oh, never mind, twt; I just realized that by asking you to reread the comments, I was asking you to REASON. And use your brain. And think. This was very silly of me.

    Here was the quote I was referring to
    "Also, using the term "IDiot" isn't very becoming of a learned individual, is it?

    It's a little embarrassing. If you claim to work according to rationality there is no need to lower yourself into schoolyard jibes. Show some respect to yourself, and others."

    So, in other words, the 'race' I was referring to was the poster's issue with the language used here, and the 'combatants' were LM and the poster. I had no particular reason to 'root for' the poster. If I have an issue with LM's words, I will mention them myself, with my OWN comment. As I have done numerous times. I don't need to piggyback on any other poster's comments to make my points.

    You called me a liar, and I have just demonstrated that you were wrong to do so. If you have even a shred of decency, you will apologize. But that is just me being silly again.

    May Fifi Be WIth You.

    ReplyDelete
  10. I recognize that I may need to clarify something, because otherwise I will probably have to yet again go through the increasingly tiresome task of explaining to twt why he is so abysmally wrong about something.

    He seems to be very hung up on the fact that I asked for an exact, or nearly exact quote of an ID proponent accusing scientists, and telling his followers to think of scientists, as 'stupid'.

    I have every expectation that ID proponents can easily be cited as calling scientists deluded, misguided, blind, etc. They undoubtedly feel that scientists misread, fail to grasp, or are in denial about, the implications of their own findings. That would be totally consistent with how they view the conclusions of scientists such as LM.

    But, 'stupid'. That is a different matter. Calling a scientist stupid would be like calling a professional athlete uncoordinated. It would be like calling a professional opera singer tone deaf. It would be challenging a prerequisite of an occupation - in this case, a high degree of intelligence.

    I find it hard to imagine that even ID proponents of any prominence would be, well, STUPID enough to do that. Of course I could be wrong, which is why I asked for a demonstration of LM's accusation. I am perfectly happy to be proven wrong. As I wrote above, I just like people to be able to back up their words.
    I would not accept examples of ID proponents calling scientists misguided, delusional, or anything like that. One can be misguided, delusional, etc. and STILL be intelligent.

    I hope that this is clear to nearly everyone here.

    ReplyDelete
    Replies
    1. ...I asked for an exact, or nearly exact quote of an ID proponent accusing scientists, and telling his followers to think of scientists, as 'stupid'.

      OK, if you really insist, here's an example ff.:

      "Stupid evolutionist"
      "Only in the feverish imagination of a stupid evolutionist"
      "Try again, stupid"
      "Arguing with stupid evolutionists is like pulling teeth"
      "You sound like that other stupid evolutionist, PZ Myers"
      "That sentence makes sense only to a stupid evolutionist"
      etc.

      I deliberately chose an ID proponent who denies equating ID with religious creationism (the "I want to discuss the design, not the designer" type, whose version of ID is a kind of intelligently directed evolution). If you follow the thread, you will see his name-calling was not provoked in any way by his opponents.

      Delete
    2. Thanks, Piotr.
      I asked, not insisted.

      Still, I am pretty sure that when LM wrote 'telling their followers that scientists are stupid' he was referring to the main proponents, not just some random hater in a comments section.

      Which is why I would prefer to have this discussion directly with him. Anyway, I'll concede in that you produced what I was asking for, because I didn't indicate my meaning clearly enough.

      Delete
    3. andyboerger says,

      I have every expectation that ID proponents can easily be cited as calling scientists deluded, misguided, blind, etc. They undoubtedly feel that scientists misread, fail to grasp, or are in denial about, the implications of their own findings. That would be totally consistent with how they view the conclusions of scientists such as LM.

      If scientists "misread, fail to grasp, or are in denial about, the implications of their own findings" is that consistent with being intelligent? There may not be many cases where creationists come right out and say that scientists are "stupid" but that's clearly what they mean.

      Intelligent people don't misunderstand their own specialty. Evolutionary biologists can't be intelligent and, at the same time, completely wrong about evolution.

      Jonathan Wells writes in "Icons of Evolution" (p. 4), "This book was written in the conviction that scientific theories in general, and Darwinian evolution in particular, can be evaluated by any intelligent person with access to the evidence."

      Wells thinks that he's an intelligent person and he finds the evidence wanting. Scientists accept that the evidence overwhelmingly supports evolution. Does that mean that scientists are also intelligent?

      Delete
    4. @Andyboeger,

      Does the quote below qualify? He does not say "stupid", but I cannot spin "is no longer considered a serious scientist or even a serious public intellectual" in any sort of positive or neutral light.

      "Probably most serious working biologists dispense with Darwinian theory in their everyday work. It simply doesn't come up, and insofar as it does, it raises manifest problems in terms of its own scientific credibility. The defense of the theory is thus left to two notable groups: the Internet atheist brigade of PZ Myers & Co. and celebrity atheists like Richard Dawkins -- who, for his part, is no longer considered a serious scientist or even a serious public intellectual -- and, curiously, to a fringe of minor academics at small religious colleges."

      David Klinghoffer August 12, 2012 7:39 AM |
      http://www.evolutionnews.org/2012/08/homework_avoida063171.html

      Delete
    5. LM asks, "If scientists "misread, fail to grasp, or are in denial about, the implications of their own findings" is that consistent with being intelligent? "

      Not consistent, but ID proponents would argue that the reason scientists do this is because they are ideologically inclined to reject 'evidence' for design in biology. A person can be very smart, and still very stubborn. Much of science history has included very smart people resisting new ideas. 'God does not play dice with the universe'. Does anyone call Einstein 'stupid'?

      You use the words stupid, idiot (lower case version as well as your own variation), dishonest, etc., quite profligately. You have given as your reason that you are fighting back. As you write,
      "You don't bring a sharp pencil to that kind of gunfight if you hope to survive. "

      Given that you excuse your own language on the grounds that you are fighting fire with fire, it follows that it would be quite easy for you to cite an example that says, or very nearly says (as I requested) that 'scientists are stupid'.

      The example that you gave from Wells is not an instance of an ID proponent telling his followers that scientists are stupid. In his quote, all he is saying is that he is writing for laymen. In other words, he is writing believing that even people without scientific degrees or backgrounds will be able to understand scientific theories if it is clearly explained to them. If that quote is typical of the rhetoric you use to justify your own use of 'stupid', 'IDiot', 'idiot', 'liar', etc. , then I would suggest that you are overreacting.

      Delete
    6. Anonymous, thanks for the Klinghoffer quotation. It made my day. I don't like Tuesdays (they are even worse than Mondays) so it's good to begin one with a good laugh.

      Delete
    7. If that quote is typical of the rhetoric you use to justify your own use of 'stupid', 'IDiot', 'idiot', 'liar', etc. , then I would suggest that you are overreacting.

      Andy, while ID supporters may be "polite" by showing proper restraint in some respects, how shall I classify this quotation to do it justice?

      "Probably most serious working biologists dispense with Darwinian theory in their everyday work. It simply doesn't come up, and insofar as it does, it raises manifest problems in terms of its own scientific credibility..."

      A lie? A fucking lie? Mendacious bullshit? "Misrepresentative propaganda" would probably be more polite, but it does not quite convey my sentiments on reading it. I hope you know by now that I do my best to respect an honest opponent, but what shall I do when confronted by a despicable liar? I'm pretty sure it wasn't written in good faith, and so this particular individual deserves no respect, as far as I am concerned.

      Delete
    8. andyboerger said:

      "'God does not play dice with the universe'. Does anyone call Einstein 'stupid'?"

      Don't tell me you're claiming that Einstein believed in "God"? That would be an ignorant claim, especially in light of the contents of a recently auctioned letter written by Einstein. You do watch the news, don't you? And what does your quote from Einstein have to do with being stupid, smart, stubborn, or resisting new ideas?

      "Given that you excuse your own language on the grounds that you are fighting fire with fire, it follows that it would be quite easy for you to cite an example that says, or very nearly says (as I requested) that 'scientists are stupid'."

      I see that you haven't looked at any of the sites I listed, and your naiveté act, whether fake or real, is really lame. Since you aren't willing to educate yourself as to what IDiot-creationists say, you're arguing and expecting from the impotent position of willful ignorance.

      Would you like to see what a very avid IDiot has said just recently? Read this page and pay attention to what joe g says, and especially what he says to olegt (a physicist) about his airplane flight:

      http://www.antievolution.org/cgi-bin/ikonboard/ikonboard.cgi?s=507d383f70ee0e93;act=ST;f=14;t=6647;st=5190

      Delete
    9. Piotr, and Anonymous;

      I think it can be instructive, and is generally a good technique for life in general, to turn a situation around.
      Suppose there is a person like Jonny who goes to an ID website and tells them not to use the kinds of quotes that Anonymous and LM have provided (from Wells and Klinghoffer), because it is unbecoming and makes them look unprofessional.
      The author of the site could reply, "well you DO know, don't you, that evolutionists are calling us idiots, stupid, liars, etc, and encouraging their followers to do the same?"
      If asked to produce evidence for this, how difficult would it be? Because of this very site, it would be as simple as shooting a fish in a barrel.
      And yet I have asked for an example of Larry's accusation of 'telling their followers that scientists are stupid' and I get
      a. hammered for it by an unhinged poster here
      b. supplied with quotes by you, Piotr, that come from an obnoxious person using the comments section, not an article or something similar that would tend to be written by someone with 'followers';
      c.LM saying 'There may not be many cases where creationists come right out and say that scientists are "stupid" but that's clearly what they mean. ', and
      d. Anonymous giving a quote, admittedly a ridiculous quote, while adding 'He does not say "stupid", but I cannot spin "is no longer considered a serious scientist or even a serious public intellectual" in any sort of positive or neutral light.'

      Am I wrong about any of this? If so, please explain why. If what I have written is basically true, please give a clear defense of why someone using words like idiot, stupid, and liar as if he bought them at a fire sale justifies doing so because 'you don't bring a sharp pencil to a gunfight if you hope to survive''?

      Where are the guns? And what does LM mean when he writes, '...if you hope to survive'?
      Survive what?

      Delete
    10. twt, see, this is why I'm almost certain you're not a scientist. I believe that any scientist would know that I used the Einstein quote to say that Einstein was very reluctant to accept the ideas of quantum physics, even though they were being validated by experimentation.

      I am not going to fill out my explanation any further. My assumption is that LM, and anyone else but you, who read my comment knew exactly what I was referring to when I wrote that.

      Delete
    11. @andyboerger

      I understood what you meant by that Einstein quotation but you shouldn't be surprised when someone reads your words quite literally and starts to nitpick at meanings.

      Pot. kettle, black.
      Houses, glass, stones.

      Delete
    12. Larry, I think I shall look long and hard before I find anything more ironic than YOU bringing up the idiom about pots calling kettles black.

      Delete
    13. @andyboerger

      We know that Larry et al. call the ID camp IDiots. Read the recent post on Wells to see why. Feel free to dislike the tactic of calling liars liars if you will, but after 150 years of this, the biology community is quite tired of it.

      You claimed "That creationists go around telling people that 'scientists are stupid' seems a bit of a stretch to me.". We supplied the evidence, from commenters in blogs, and from the big boys. Yes, they do. So your narrative of the poor denigrated ID-supporter-community that just wants to have a serious dialogue has some problems.

      Clear?

      Delete
    14. Anonymous, that's a straw man. Not once did I refer to a poor, denigrated ID supporter-community wanting to have a serious dialogue. I referred to ID leaders probably not being so bold as to come right out and say that scientists are 'stupid', a very harsh word( that I note that LM throws around with abandon). My issue has been with unnecessary rhetoric all along, specifically overreaction and justifying ones own behavior because of the other side. Etc.
      I asked for evidence of this, and many here have taken the time and trouble to provide it. None of us want to spend the rest of our lives arguing about this. I will accept what you have provided as more or less satisfactory, but continue to have quibbles about it that can only be interpreted from this side of the fence as being overly nitpicky. I'll swallow that.

      Delete
    15. I think it can be instructive, and is generally a good technique for life in general, to turn a situation around.

      A situation is easier to turn round if it's symmetrical. In the science vs. ID debate, it isn't. To begin with, ID itself is one monumental deception, a ploy designed to give creationism a scientific-looking façade and a false respectability. Creationism tries to masquerade as science in order to promote its aggressive agenda, and in particular to introduce "teaching the controversy" into school curricula. Do you wonder why scientists resent such Trojan Horse tactics? The Klinghoffer quote above may look "ridiculous", but remember that Klighoffer is a PROMINENT ideologue of the ID movement, he has lots of FOLLOWERS and his ridiculous propaganda can do a lot of very real harm. In the US, at least, it's a real culture war, and the future of the educational system is at stake.

      I have no such problems at home. In my country, according to recent surveys, some 50% of the population accept evolution as a fact, 30% believe in some form of creationinsm, and the remaining 20% just don't know. Among the younger generation, however, the proportion is roughly 70%-20%, and that in a country where nearly 90% of the population define themselves as nominally Roman Catholic. Most of the local creationists are too ignorant to have an informed opinion on anything scientific. The ID movement is very weak here, with no supporters in the academia. It's sponsored mainly by the Watchtower Society, and I don't think Catholics are likely to trust an American import associated with Jehovah's Witnesses. That's why I can take it easy, but I understand why in other countries the debate easily turns into a "gunfight".

      Delete
    16. Piotr, I think that's an excellent point. I truly do. In fact, I concede it without reservation.

      But then, how would you imagine that using terms like IDiot, idiot, stupid, liar, etc. etc. is going to help turn the battle around? If the ID PR team is as strong as you say they are (not disputing this), then what could be easier for them than to turn their followers' attention to this very site and say, 'do you see how vicious the people we are up against are'? Larry talks about 'gunfights', but I would say his type of OTT rhetoric, to say nothing of twt's, is providing those 'guns' with fresh rounds of ammunition.

      Delete
    17. @ andyboerger

      Apologies if I read to much into your comment (straw man accusation). That was my actual understanding of your stance, and not a deliberate straw man.

      So I retract that last sentence about the "poor denigrated ID-supporter-community".

      Delete
    18. andyboerger says,

      If the ID PR team is as strong as you say they are (not disputing this), then what could be easier for them than to turn their followers' attention to this very site and say, 'do you see how vicious the people we are up against are'?

      That's exactly what they do. It means I get all kinds of IDiots reading my posts. Many of them come here to argue about evolution. Some of them even learn something.

      Meanwhile, the polite, accommodationist, science blogs are ignored. They never get mentioned on any of the creationist web sites.

      You don't have much experience with trying to drive social change in the face of irrational, bigoted, opposition, do you?

      Delete
    19. But then, how would you imagine that using terms like IDiot, idiot, stupid, liar, etc. etc. is going to help turn the battle around?

      I don't know, perhaps it isn't. But scientists are busy people. They have classes to teach, student papers to correct, articles to write, lab work to supervise, administrative chores to do, libraries to visit, etc., etc. Most of them don't even think of confronting pseudoscience -- it's unrewarding, frustrating as well as time-consuming. What can you say to a fellow who comes along and demands a one-paraghaph-long "irrefutable proof" that modern biology is right and creationism is wrong? Leisure activities like blogging are done in stolen time, so one is naturally tempted to tell the intruder to sod off at once, especially if his reactions are predictable. Even if you devote an hour of your time and a lot of good faith to provide him with expert info, he won't understand, let alone remember, any of it. Not necessarily because he is stupid but because in typical cases the purpose of his visit is to piss on your turf, not to learn anything.

      All that said, I have to add that it wouldn't be fair to generalise. I have had interesting and entirely civil discussions with creationists who were genuinely interested in the opinions and arguments of mainstream science. In such cases I feel my time is not completely wasted: gutta cavat lapidem.

      Delete
    20. I have had interesting and entirely civil discussions with creationists who were genuinely interested in the opinions and arguments of mainstream science. In such cases I feel my time is not completely wasted: gutta cavat lapidem.

      There's a big difference between dealing with individuals one-on-one and fighting the battle in the public sphere. I behave very differently when I'm talking to a creationist in my office or in a pub.

      So do they.

      Delete
    21. LM asks
      'You don't have much experience with trying to drive social change in the face of irrational, bigoted, opposition, do you? '

      No, I don't. But I have had numerous life experiences, many of them involving conflict, and I try to never use an opponent's tactics to excuse my own (I don't always succeed at this), because I don't want to become that which I am opposed to.

      That said, although I disagree with your approach, I respect it as something you are committed to. Moreover, I truly appreciate the fact that you have created this site as an open forum, and have allowed me the freedom to air my criticisms without restriction.

      Delete
    22. andyboerger said:

      "Where are the guns? And what does LM mean when he writes, '...if you hope to survive'?
      Survive what?"

      You call yourself a writer, yet you don't recognize a metaphor?

      No wonder you're an IDiot-creationist. You go to great lengths to insure that you're totally ignorant of the behavior and agenda of many of your fellow designer-creator-spirit-god pushers. Even when you're presented with a revealing trail to follow you close your eyes and put your fingers in your ears and just keep spouting the same stupid, ignorant, and/or dishonest arguments and demands.

      When someone willfully resists becoming informed, as much as you do, it's no longer a matter where they can justify the 'Nobody told me' excuse. The only person stopping you from being informed is you, and the same thing applies to all the other ignorant IDiot-creationists.

      You insistently and nitpickingly expect people (actually just the people you disagree with) to be able to back up their words with exact quotes or other concrete evidence, even when they're just making generalized, CLOSE ENOUGH comments, but you don't apply that expectation to yourself or your fellow creationists. You also conveniently ignore exact quotes or other evidence or trails to evidence and you move the goalposts so that you can try to get away with claiming that the quotes or other evidence don't reasonably fulfill your requests (actually insistent, nitpicking demands).

      Your arguments are based on willful ignorance (or dishonesty, or both), blindly defending your fellow IDiot-creationists, playing games, and pushing your creationist beliefs. You'd be wise to listen and learn a lot more and keep quiet unless and until you actually have a clue, if ever.



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    23. twt asks,
      "You call yourself a writer, yet you don't recognize a metaphor? "

      Yes, I call myself a writer, because it's my job, and of course I recognize a metaphor, silly.

      As for you, you call yourself a .......what do you call yourself?

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  11. andyboerger said:

    "Still, I am pretty sure that when LM wrote 'telling their followers that scientists are stupid' he was referring to the main proponents, not just some random hater in a comments section."

    You just don't know when to quit playing games, do you? Now you're moving the goalposts again with "main proponents" versus "some random hater in a comments section". The point Larry made is accurate and the words he chose were CLOSE ENOUGH no matter which particular ignorant amateurs (aka IDiot- creationists) he was referring to.

    Are you ever going to make any points that actually matter or are you just going to keep on nitpicking generalized comments and moving the goal posts for the sake of being an argumentative prick?

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  12. "I find it hard to imagine that even ID proponents of any prominence would be, well, STUPID enough to do that."

    Now you're expecting an exact quote of a 'prominent' IDiot directly calling scientists "stupid".

    Man oh man, those goal posts are headed for deep space. Where did Larry use the word "prominence"? Do you think that because he used the word "followers", it absolutely requires the ignorant amateurs to be 'prominent'? Shit, even denyse o'leary has "followers" but I'd hardly call her prominent. She's just an IDiotic catholic cult lunatic that most of the world has never heard of.

    "Of course I could be wrong, which is why I asked for a demonstration of LM's accusation. I am perfectly happy to be proven wrong. As I wrote above, I just like people to be able to back up their words."

    No, you asked for a quote, but now you'll settle for a "demonstration", eh? Well then, read everything I suggested above, especially if you would be really happy to be proven wrong. Isn't it time for you to educate yourself on what IDiot-creationists say before you dig your hole any deeper?

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    1. "Where did Larry use the word "prominence"? Do you think that because he used the word "followers", it absolutely requires the ignorant amateurs to be 'prominent'?"

      A good question. I am stunned.

      Yes, that is exactly why I used that word. I would expect that they would be people who have a well visited site, give speeches, perhaps a talk or two on youtube, etc. Otherwise, very doubtful that they will have followers. If they don't have followers, then obviously Larry wasn't referring to them.

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  13. Re: "Note that biological evolution refers to populations and not to individuals. In other words, populations evolve but individuals do not. This is a very important point. It distinguishes biological evolution from other forms of evolution in science (e.g., stellar evolution)."

    The problem is that most things which are classified as "individuals" consist of populations which do, in point of fact, evolve. For example, individual animals consist of populations of cells - which themselves evolve over multiple cell generations. So: evolution can't realistically be excluded from individuals in the way that you propose.

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  14. Since this misunderstanding appears to be so widespread, I wrote an article about it, titled: "The neo-Darwinian dogma that individuals do not evolve".

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    1. You accuse me of being a "neo-Darwinist"! Don't you think that's a tiny bit ridiculous?

      Here's the link to your rather idiosyncratic view of evolution: The neo-Darwinian dogma that individuals do not evolve. I'll grant you this: it fits in nicely with many of your other beliefs.

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    2. Larry, I didn't accuse you of being a "neo-Darwinist". Just because a group has a shared belief, it doesn't necessarily imply that everyone with the belief identifies with that group.

      You don't bother with defending your position. IMO, that's probably because it's mistaken. Darwinian individuals often consist of populations (e.g. of cells), which themselves evolve via Darwinian mechanisms - including natural selection. This has been recognized since Gerald Edelman's work on the immune system in the 1960s.

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    3. Larry, I didn't accuse you of being a "neo-Darwinist".

      Tim, the title of your post is, "The neo-Darwinian dogma that individuals do not evolve." Then you quoted my definition,

      You don't bother with defending your position.

      I defined biological evolution. That definition excludes the examples you use in your post. That's because 99.99% of biologists do not think that the formation of a cancer cell is an example of biological evolution. They also don't think that the development of humans from a zygote to an embryo to a fetus, to an adult is an example of biological evolution. That's the only defense that matters when we're talking about definitions.

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    4. You appear to be misremembering - I never quoted your definition.

      Nor do you get to pick examples in this discussion. Some types of development don't count as being evolutionary. For example, clonal expansion results in no change in gene frequencies. Such cases are pretty irrelevant to this discussion.

      The point is that some sorts of development are evolutionary - and are well modeled by Darwinism. The most relevant cases are those where gene frequencies iteratively change in a population. This has been demonstrated in the case of clonal selection in the immune system. The effect is part of what is commonly known as "somatic evolution" - which is a widely-recognized phenomenon these days.

      It should be said that understanding of Darwinian evolution of cells within individuals was a relatively recent development. It wasn't recognized until the 1960s. These days knowledge of it is much more widespread - and the somatic evolution of cells within individuals is often given as a standard example of multi-level selection.

      It is odd to hear someone denying that reproduction with variation and differential reproductive success in a population of cells over multiple generations *doesn't* count as an instance of Darwinian evolution. It would seem that - according to your own definition - it clearly does.

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