Sunday, June 24, 2012

Do the IDiots Understand Evolution?

David Klinghoffer noted recently that an anthropologist, Richard Leakey, and some lawyer named Jonathan H. Adler seem to be using different meanings of the word "evolution" [For Richard Leakey and So Many Other Darwin Advocates, Evolution Is a Word that Can Mean Anything]. It doesn't seem to matter to Klinghoffer that one of those men is a scientist and the other isn't.

Picking up on the point that evolution is a word that can mean anything, Joshua Youngkin1 adds his 2 cents [On the Useful Instability of the Word "Evolution"].
David's concern, I think, is that Darwinists use the term "evolution" in various and even conflicting ways in order to occasionally serve less-than-noble purposes. It's almost as if Darwinist usage of the term "evolution" is sometimes meant to keep skeptics and even the public guessing, as if to avoid a fair fight on the evidence about a stable, commonly understood set of propositions. Why would anyone want to do that?
The meanings of the word "evolution" can be found in evolutionary biology textbooks and at many places on the web. You can read two of my contributions at What Is Evolution? and Evolution Is a Fact and a Theory. It seems to me that many evolutionary biologists are making a very serious effort to define their terms.

Some of the IDiots actually get it as I pointed out a few weeks ago [All IDiots Believe in Evolution!]. That was in response to a posting by johnnyb who said ....
So what is one to do? Well, thankfully, our friends the evolutionists have given us a way out. In their zeal to claim consensus on the “fact of evolution,” they have had to steamroll together such a large diversity of opinion into the single term “evolution”, that the word “evolution” no longer has the grand meaning it used to. The only real meaning everyone can agree on is “change in allele frequency over time” – and that is a definition that literally everyone can agree with.
Apparently his fellow IDiots didn't get the memo.

It doesn't take a lot of effort to recognize what evolutionary biologists mean when they use the word "evolution." You have to be really stupid to imagine that they are deliberately using different meanings in in different contexts for the sole purpose of confusing the IDiots. As you can see, the IDiots are quite capable of confusing themselves without our help.

Speaking of deliberate obfuscation ... I wonder why they continue to refer to "Darwinists" when they've been told hundreds of times that this is not a synonym for "evolutionary biologists"? Is that for a "less-than-noble purpose" or is it just because the IDiots are stupid? I think we know the answer to that one.

I have some sympathy for bloggers who are ignorant but I don't like liars. However, the people I really hate are the hypocrites.


1. Joshua Youngkin is a lawyer who works for the Discovery Institute. He's probably an expert on the meaning of the word evolution.

54 comments :

  1. Larry, do you understand the distinction between evolution (gradual change over time) and origination? I don't think you actually do.

    All things will inevitably change, be they living organisms, political systems, technology, economies, galaxies..whatever. Nobody is in any doubt about this fact.

    But how something evolves does not necessarily explain how something came to exist in the first instance. We can talk about the evolution of the beaks of finches, or of the sequences of introns, but this doesn't account for their origins. Creationists maintain that evolution, be it Darwinian or otherwise, can never provide anything close to an answer for this.

    ReplyDelete
    Replies
    1. Are you postulating a special creation for beaks? If so, you will have to go back quite a way. As far as Protoceratops for instance.

      Am I right in thinking that, if a credible evolutionary origin of beaks from some precursor were established, you would simply demand an explanation for the precursor? If so, you might just as well say "You can't explain the big bang" and save us all a lot of trouble.

      Delete
    2. How can you possibly claim that organisms can change, but just not that much? Beaks can change shape, but they can't originate. Skin can become scalier, but it can't become scaly. Hairs can become coarser, but a creature can't become hairy.

      Hows it work for bird flight? Were they created with /enough/ of an incipient wing with incipient feathers, that they could then eventually evolve into full feathered wings? But nothing without an incipient feather can ever develop incipient feathers? Variation, just not that much?

      Delete
    3. Of course I can. There are limits to biological change just like there are limits to anything. Yes, beaks can vary in shape and size - and this can be attributed to changes in growth and transcription factors etc. - but it is does not provide any insight as to how beaks came into existence.

      As I have repeatedly remonstrated on this site, organismic features like beaks, feathers and skin are not encoded in the genome even if the proteins used in them (like keratins) are.

      Delete
    4. There are no limits to certain infinite series, such as 1 + 1 + 1 + .... Mutations keep adding up indefinitely like this. Populations which does not become extinct, keep evolving indefinitely.

      Delete
  2. I agree with the creationists. Evolution is not the same as the origin of life.

    How do the creationists know that science will never be able to account for the origin of life?

    ReplyDelete
    Replies
    1. I think Atheistoclast is talking about the origin of novel traits, not the origin of life. But, that's obviously wrong too. A quick search on Google Scholar shows that we know quite a bit about the cranio-facial development and evolution in birds, including the beak (a recent e.g. http://www.nature.com/nature/journal/vaop/ncurrent/full/nature11146.html).

      This style of argument (i.e. accepting microevolution, but not macroevolution) seems to have become increasingly common in creationist argument in the last 10 - 15 years. Creationists want micro and macro to be a black and white distinction, when they're really just convenient terms for relative positions on a spectrum of evolutionary change.

      Delete
    2. Creationists actually accept "macro-evolution" if it is defined as "speciation" - the emergence of a new species. Creationists maintain, for example, that wolves and coyotes evolved from a common canid "kind". What creationists do not accept is universal common ancestry and the origination of novel traits through tinkering and modification.

      The paper you cite in Nature is little more than an interesting observation and a lot of speculation besides. It presents no evidence whatsoever of the inferred molecular changes believed to be responsible for the alleged paedomorphic development in birds as compared with reptiles.

      Delete
    3. Darwin called his famous book "on the Origin of Species." He did not call it "on the Evolution of Species". There is a potentially important difference between these two titles. One purports to explain how all species emerged about through a process of universal common "descent by modification". The other could just refer to the ongoing small changes that inevitably happen over time (such as variations in the beaks of finches). The creationist can accept the latter but not the former.

      Delete
    4. The nature paper was just one example. If you're only interested in molecular changes, try putting 'BMP-4' and 'birds' into Google Scholar. BMP-4 is not the complete story, but it'll get you started.

      Delete
  3. Larry, I think that creationists (and "ID theorists, which is almost the same thing) all accept that "evolution" happens. But it was not always so. 100 years ago they were insisting on the Fixity Of Species, and resisting the idea that species could change. That had been a view biologists accepted earlier, about 100 years before that. It was only fairly recently (I'd say the past 30 years) that creationists caved in and accepted that a population could change. It represents major backpedalling on their part.

    As for calling evolutionary biologists "Darwinists", that is not stupidity on their part, but "framing". If they can get the public to accept that we adhere to an "ism" then they can make us out to be cultists who are not doing science. I think the Discovery Institute played a large role in popularizing the label "Darwinist".

    ReplyDelete
  4. I should add that it is not really true that creationists agree that Origin Of Life is not the same as evolution. When they are arguing that no one disagrees with "evolution", they do distinguish between the two.

    But when Stephen Meyer (in his book Signature In The Cell) starts talking about the origin of biological information, he wobbles back and forth between the OOL and subsequent change of lineages. He makes little distinction between them in the book, and as a result leaves total confusion in his wake.

    Whether the two are said to be conceptually distinct depends on the momentary needs of the creationist argument.

    ReplyDelete
    Replies
    1. The origin of biological information and the origin of life are not synonymous - although they are related. Clearly, new information, in the form of new genes and regulatory sequences, have been added to genomes since the time of the LUCA. People like yourself propose that this important development is nothing more astounding than the result of variation and differential reproduction at the molecular level. I request that you provide some evidence in support of your assertion.

      Delete
    2. Once the basics of information inheritance are in place (DNA/RNA replication machinery, cellular replication), new genes and regulatory sequences can readily arise by duplication errors. Once infectious genetic elements (viruses, conjugative plasmids) and DNA uptake processes are common, new information can enter genomes readily by horizontal transfer without the need for dedicated mechanisms. Evidence supporting these statements is available in any basic genetics textbook.

      Delete
    3. Nonsense. The idea that gene duplication events can generate new information has been thoroughly debunked and refuted:

      http://onlinelibrary.wiley.com/doi/10.1002/cplx.20365/abstract

      I have never read of a retroviral insertion becoming a new functional gene but there is some evidence that they can influence gene expression.

      Delete
    4. Please tell everyone what definition of "information" you're using here. That might be important to your point.

      Delete
    5. Atheistoclast,

      Obviously you have no idea of what information is, because a gene duplication is immediately and unambiguously new information. But it gets worse for you, because gene duplications have been demonstrated to change and add other kinds of information in experimental situations, such as those requiring certain genes to change their specificities, where the quite common case of random tandem duplication makes the trick, often ending, after mutations and gene recombinations, with at least two genes, each with different substrate specificities (one original, the other new), new information by any standard. So saying that new information by gene duplication is nonsense reveals plain ignorance of both, the meaning of information, and the studies showing that this happens both in nature and in experimental settings.

      Worse, you are stupid enough to think that because a couple of authors gathered data that did not show spectacular changes, thus no duplications will make for more prominent changes. Their limited knowledge did not allow them to note a few examples, such as yeast adaptations to aerobic and anaerobic lifestyles (involving lots of duplications), or the added complexity of development by multiplied transcription factors across eukaryotes. But that just means that these authors were unable to see beyond their limited data, not that duplications have been debunked as able to add information.

      There is much more than that, so, as most creationists, you use an authoritative tone to try and disguise that your conclusions follow from carefully ignored evidence and misread abstracts.

      Delete
    6. Ha! That's rich. That paper is a commentary (i.e. essentially an opinion piece) that has never been cited, provides no new data and conflicts with empirical evidence showing the prevalence of novel function in duplicate genes. It's hardly even a contribution, let alone a thorough debunking and refutation of evolution by gene duplication. And you have the temerity to accuse others of nonsense.

      Delete
    7. I think the "cited by" tab says it all... no one but you believes your arguments in that essay.

      Delete
    8. Atheistoclast wrote that paper himself.

      Delete
    9. @ Negative Entropy:

      1. A copy of something is not new "information". It is, however, new physical "data". We are not any more "informed" by the repeating of the same message.

      2. Gene duplicates do change because they are liable to degenerate due to a relaxation of purifying selection.

      3. Most duplicate pairs end up "subfunctionalizing". They divide their information content between one another.

      Delete
    10. This comment has been removed by the author.

      Delete
    11. Atheistoclast,

      1. A copy is of course new information. You need energy to produce such copy. As I said, you have to be too ignorant about what information is in order to declare that gene copies don;t add new information. Even reproduction adds new information into the environment.

      2. Changes are also new information.

      3. I told you ass-hole, experiments show changes of activities, not subfunctionalizations, but new activities, new recognitions, et cetera.

      4. If you wrote that "article" I wonder how could you mistake your own words from lack of observed spectacular examples in the limited data you decided to use, for "thoroughly debunked."

      You show again a complete lack of understanding and wilful ignorance. Not that I am surprised. Your attitude is classic creationism: cherry-pick, misread, mislead, and declare victory. Next you will smell your own ass and conclude that an intelligent designer put amazing ideas in there for you to display.

      Delete
    12. Atheistoclast: Still don't know what "information" means. Lacking a definition, your comments only confuse the question. You clearly aren't using Shannon information. But what are you using?

      Delete
    13. John, "Information" in the context of molecular biology refers to the instructions encoded in DNA that confer biochemical function. Shannon defined information as the "reduction of uncertainty". Biological information is precisely that - it reduces uncertainty by providing specificity. I suggest you read this paper:

      http://octavia.zoology.washington.edu/publications/GodfreySmith11.pdf

      Delete
    14. Negative entropy,

      1. No a copy is not new information: GO TO BED GO TO BED GO TO BED contains no more information than GO TO BED.

      2.Changes often scramble existing information.

      3. No, they show slight modifications to pre-existing activities.

      4. The examples provided are some of the most cited.

      5. Nope, I surveyed most of the literature. Most scientists would agree with me that gene duplication does not explain the origins of the really important molecular features, notably protein motifs and regulatory sequences.

      Delete
    15. Your definition is too vague to be useful. Another failing is that it isn't at all quantitative. If you can't quantify information, how do you know whether it's increased? And you've already claimed that both gains and losses of specificity are reductions in information.

      Delete
    16. That is because information is fundamentally qualitative in nature. However, some aspects of biochemical information may be quantitative - such as the catalytic properties and reaction rates of enzymes.

      Delete
    17. You can't compare a qualitative feature saying it has increased or decreased over time: it would be meaningless.
      On the other hand, you can easily define a quantitative measure of information contained in the genome (it requires just a conversion from the base 4 to the base 2). Unfortunately, the quantitative measure of information thus defined does not support your claims. Too bad for your claims (you may still cherrypick the other possibility, namely "too bad for the qualitative measure of information", in order to "save" your claims from being duly rejected).

      Delete
    18. Atheistoclast,

      It is incredibly stupid to suggest someone to read that shit for definitions and understanding of information when there's this:

      http://www.ccrnp.ncifcrf.gov/~toms/

      Which by the way has there an article showing how easily and readily new regulatory sequences can evolve. (Nobody said that duplications explained every case of increased information you ass-hole.)

      So, obviously you did not read any literature, but whatever lead to your conclusions. Gene duplication is not the whole story, but it does increase information readily. If you gather the strength to read and understand Schneider's articles you might figure out how wrong you are. Maybe you need to go beyond definitions and into the equations. Maybe you need to go into the connection between energy and information. Maybe there is a lot you have no idea about.

      1. Copies are certainly more information. "GO TO BED GO TO BED GO TO BED " has more information than GO TO BED. The former required more energy to be written, but I do not need to explain that. Try to describe them and make those descriptions into bits and you will see that you need more bits to describe the first than the second. So, that soon you have been proven both wrong and ignorant about information.

      2. That changes can scramble existing information does not mean that changes are not new information. Try and describe both, the original and the changed copy into bits ... ups!

      3. Nope, they change activities in important ways. If a bacterium is able to not just resist, but eat antibiotics with a mutated gene, then that's new activities and new information. WIll you claim that because you despise the ability to eat lactose as "just another sugar" then lactase is not important information for survival when lactose is what's available? Are you that much of an ass-hole? (Oh. My bad. Sure you are that kind of an ass-hole.)

      4. Whether your examples are among the most cited or not is inconsequential, your abstract does not read as "thoroughly" debunking and refuting anything. It reads as not finding spectacular changes but finding new information nonetheless. Whether your examples are the most cited or not does not mean that you did not distort anything. With the careless way you distorted here the conclusions of an article you wrote yourself, why should I trust that you did not distort other articles you cited therein?

      5. Besides experimental evolution, I have already listed a couple well-known examples that you missed that show spectacular new stuff from duplications, which you conveniently ignored. Seems like your claims are the ones that have been thoroughly debunked and refuted.

      Delete
  5. A major problem with the creationists, and especially so with the advocates of "Intelligent Design", is that they don't give a description of what their alternative is to evolutionary biology. What happened and when, where, how? What would it look like if we saw a creation/design event taking place? What was the precursor of the created/designed thing? Give us an example of something (even something hypothetical) that is not created/designed. What properties of the designer(s) or constraints on the material they were working with led them to make the designs that they chose? Do they have anything to say other than "somehow, something must be wrong with evolutionary biology"?

    TomS

    ReplyDelete
  6. Creationists these days commonly claim they accept microevolution, but then the same creationist will sometimes turn around and attack various microevolutionary processes: natural selection is a tautology, peppered moth experiments are fraudulent, favorable mutations can't happen, etc. But that's OK; it's only a problem if you expect logical consistency, and that's not an issue with them.

    ReplyDelete
    Replies
    1. No, most creationists have accepted that there are mutations which are "beneficial" with respect to reproductive fitness, but which nonetheless often involve a loss of function. The classic example is less permeable outer membranes in bacteria providing resistance to antibiotics.

      Delete
    2. Oddly enough, if bacteria evolved a more permeable membrane, creationists would consider that a loss of specificity, and therefore a loss of function. And birds lost the function of being unable to fly. It's just so easy when you know how to think about it.

      Delete
    3. You're right. A membrane that allowed in stuff that it should not would indeed be an example of a structure that had lost its functional specificity.

      Delete
    4. So a less permeable membrane is a loss of function, and a more permeable membrane is a loss of function too. Why not just admit that every conceivable change is a loss of function?

      Delete
    5. Yes, John, the vast majority of mutations involve a loss of function. Often it is very slight, but can be very large.

      Delete
    6. Please don't say "yes" and follow it with something quite different from what I said. That's cheesy.

      How about this one:

      1. Molecular evolution is reversible.
      2. Mutations can lose information.
      3. Therefore, the reverse mutation can gain information.

      Delete
    7. A-clast:
      "Yes, John, the vast majority of mutations involve a loss of function. Often it is very slight, but can be very large."


      Actually, the vast majority of mutations are neutral or nearly so.
      I would also add that beneficial mutations can also produce effects that are "very slight, but can be very large."

      Delete
    8. I notice that you fail to provide any citation to support your assertion. You are wrong. The vast majority of mutations are slightly deleterious with respect to reproductive fitness. Hardly any have a selection coefficient of s=0.0.

      http://rstb.royalsocietypublishing.org/content/365/1544/1177.full

      As predicted, most of our lines decreased in fitness, supporting the notion that the vast majority of mutations are deleterious

      Delete
    9. Wrong. That method doesn't even consider neutral mutations. And in fact, "The overall mutation rate in this mutator strain is expected to be 0.18 per genome per generation (based on the mutation rate for wild-type E. coli (Drake et al. 1998) and on the measured mutator strength), which is 36 times higher than the Ud estimated in our experiments. This implies that the majority of mutations are effectively neutral in our experiments or that we do not have the power to measure many of them, which is in full agreement with previous indications from other organisms that the distribution of sd is very leptokurtic."

      Further, I bet anonymous was thinking about eukaryotes, which have large amounts of junk DNA.

      Delete
    10. Like I say, hardly any mutations are expected to incur a selection coefficient of exactly s=0.0 (i.e. be completely neutral). The vast majority of mutations are therefore predicted and observed to be slightly deleterious. This applies to both coding DNA and ncDNA. Here is a paper on mutations in the nematode that confirms this:

      http://www.indiana.edu/~lynchlab/PDF/Lynch138.pdf

      In accordance with evidence that the vast majority of mutations are deleterious....

      There is no escaping this unquestionable fact.

      Delete
    11. So it doesn't bother you at all that your citations don't support your point? You're just quotemining. And your new reference is talking about, and assaying, only those mutations with a detectable phenotypic effect. It isn't screening for silent mutations at all, which is where we would expect the bulk of neutral mutations to be. Have you no shame? No, don't answer that.

      Delete
    12. No, I am not quote-mining. I have cited two papers that show that the majority of mutations are slightly deleterious where the phenotypic effect is detectable. As for "silent mutations" you should know that years ago it was shown that many "synonymous mutations" believed to be innocuous can adversely affect mRNA stability.

      http://www.brighthub.com/science/genetics/articles/39340.aspx

      Here is another paper that finds that most amino acid substitutions in gene products are "strongly deleterious".

      http://homepages.ed.ac.uk/eang33/publications/eyrewalkeretal20022.pdf

      Enjoy.

      Delete
    13. I have cited two papers that show that the majority of mutations are slightly deleterious where the phenotypic effect is detectable.

      The idea that something being "detectable" could have that kind of effect is pretty interesting. What in nature is doing the "detecting" in this case? Does the act of "detection" not really refer to scientists who, by detecting an effect transform that into a "phenotypic" trait? I wonder, before the evolution of eyesight, were traits that become "phenotypic" with that sense of a truly different kind before that was possible and what that means for this distinction.

      That's a matter of curiosity, only. It doesn't imply anything about the reality of evolution, which is a fact, it might, though, imply a lot about the scientific study of it.

      Delete
  7. "I would love to sit down with a guy like Jonathan H. Adler, who teaches law at Case Western Reserve University, and quiz him on what he thinks evolution entails," says David Klinghoffer. And I'd love to watch him get creamed as Adler joins forces with his colleague across Euclid Av. - Dr. Patricia Princehouse. No I don't think David wants to go to Cleveland. No.

    ReplyDelete
  8. How do the creationists know that science will never be able to account for the origin of life? LM

    A better question is how science will ever be able to know if it has accounted for the origin of life without any evidence of that event. How will it know it hasn't described something very different from that event?

    What do you mean by science "accounting for the origin of life", if not a reliably accurate description of that event as it actually happened? That's a problem that is far, far more difficult than accounting for paleolithic behavior among early human populations and science can't really do that, either.

    What if "science" comes up with more than one account of "the origin of life"? Which is what is almost certain to happen.

    ReplyDelete
  9. especially so with the advocates of "Intelligent Design", is that they don't give a description of what their alternative is to evolutionary biology. Anonymous.

    Now, here is an example of someone not understanding that you can believe that evolution, as it happened, in every detail is an intelligent design.

    A very large percentage, I'd guess most, of the people who accept evolution believe something like that, though they might also realize that their belief isn't a part of science, proper.

    It would be really helpful if scientists were more specific about what is said about science that is science, proper, and science, not exactly. It might help the laity from being confused.

    ReplyDelete
    Replies
    1. Oh, I know perfectly well that "Intelligent Design" doesn't say anything at all, so that it is compatible with anything, including evolution. ID, in all of its vacuity, does get a bit tedious.

      Delete
    2. See, one of the problems that science has is that people don't distinguish between what is a legitimate scientific idea and what is a legitimate idea OUTSIDE of science.

      Intelligent design as a philosophical or religious idea is legitimate, it's not legitimate within science because of technical requirements. You could say the same thing about materialism and any other philosphical, religious, political, ideas that are far more likely to be successfully and illegitimately asserted as science. Which is the entire basis of the atheist fad of the past decade and much of the junk that was once current as science and now can only be held to have been mistaken as being "science". Scientific racism, sexism, eugenics, etc. are all examples of that. When I look at who wants to bring some of them back today, I'm struck at how many of those within science are materialists who want to plug their ideological ideas into science. Many within cog-sci, and the various parts of the so-called sciences that have successfully invaded the real science of evolution. All to no to little objection among the materialists.

      Delete
  10. As Atheistoclast points out, only reduction in information is possible, so only simplification of the originally created "kinds" can occur, resulting in the toverwhelming tendency toward ever simpler forms through time we clearly see in the fossil recor - oh, wait....

    ReplyDelete
    Replies
    1. Well, if one would admit that the ultimate result of the evolutionary process is Atheistoclast himself, his considerations would be actually consistent with his display on here: he shows a blatant lack of information and a clear inability to step towards higher & more complex levels of understanding.

      More seriously, it is obvious that when he writes "GO TO BED GO TO BED GO TO BED contains no more information than GO TO BED" he completely forgets about counting: even without getting into deeper computations it is easy to note that the string "GO TO BED" contains a certain message encoded in words with meaning, while the string "GO TO BED GO TO BED GO TO BED" contains the same message plus the supplementary information that it is repeated three times, which constitutes of course new information. Moreover, if instead of English words we think about initially perfect duplication of a gene, the mutations will affect differently the two copies (unless some very unlikely scenario happens and they both follow the same more or less random process) and they will tend to accumulate more and more information (of the kind "the n-th nucleotide is no longer an A but a C in the copied gene") over the time. Ultimately, after a long evolutionary time, the two genes could code for radically different proteins having also unrelated functions, that is the information increase would correspond to new different "meanings".

      Delete
    2. By the way, lest there be any confusion, I am not arguing for a view of evolution as tending toward ever more complex forms over time. Both gains and losses of form and function occur over time via evolution and the processes that affect it, like contingency.

      The only overall tendency in all of this is one Stephen Jay Gould described in his book Full House. Since anything more simple than the simplest forms of life is not life, the "tree" of life is more like a bush growing against a wall. It can branch in the direction of equal or more complexity, but not of less or else it isn't life any more. Thus by far the greatest result of evolution is life of complexity equal to, not greater than, the ancestral forms. There are occasional outbreaks of greater complexity, like onions, salamanders, and to a lesser extent (at least based on genome size), us.

      Delete
  11. Why does the DI need so many lawyers?

    ReplyDelete