55 Responses to “Mitochondria in charge?”

1. Bradford Says:
   April 26th, 2008 at 10:48 pm

   From the link:

   "From unicellular yeast to complex mammals, the process is the same," Bryk said. "The job of a cell is to divide and grow. Metabolism takes in "˜food' and turns it into fuel and building blocks for DNA replication and gene expression."

   When I read things like this I wonder what it would have been like just prior to the advent of mitochondria? If mitochondria are a cell division command center then where was the eukaryotic command center prior to mitochondria or if one says really Bradford, eukaryotic cells became so because of mitochondria, this just raises other questions.

   But when these processes falter, diseases can result. Too much cell division too quickly, for example, is typical of cancerous cells, Polymenis pointed out. Conversely, poor metabolism "“ stemming from mitochondrial deficiencies "“ is at the root of damage to various organs such as the brain, heart, skeletal muscles and liver.

   Mitochondrial malfunction increasingly is being recognized as a source of disease and cancer. Interesting finding.

Comment by Bradford — April 26, 2008 @ 10:48 pm

2. AnaxagorasRules Says:
   April 27th, 2008 at 12:19 am

   Hi, Bradford,

   When I read things like this I wonder what it would have been like just prior to the advent of mitochondria?

   Another thing I wonder about is how can any cellular component that has its own DNA and RNA be thought not to have command and control abilities? And another thing, I've read that because Mitochondria have similarities with a specific group of bacteria (the purple bacteria phylum), and because mitochondrial DNA is similar to that found in bacterial cells, it is thought that mitochondria arose from bacteria that invaded the ancestors of plant and animal cells.

   My rudimentary knowledge of biology questions this reasoning. In fact, it sounds like a bunch of whacked out BS. Just how the heck does something the size of a mitochondrion get through a cell's plasma membrane in the first place? Protiens and solutes and ions get through the membrane, not entire organisms, for crying out loud! Unless bacteria have some sort of magical open sesame key. Of course, I'm no bacteria expert.

Comment by AnaxagorasRules — April 27, 2008 @ 12:19 am

3. nobody Says:
   April 27th, 2008 at 5:49 am

   In conclusion, the control of DNA replication by an increase in mtDNA we describe here suggests that the mitochondrion does not simply provide the energy at the service of its larger cellular host, but it may actively dictate when cells initiate their division. Furthermore, metabolic control of chromatin modifications may provide critical links between metabolism and cell division.

Comment by nobody — April 27, 2008 @ 5:49 am

4. nobody Says:
   April 27th, 2008 at 5:52 am

   http://www.plosgenetics.org/ar...

Comment by nobody — April 27, 2008 @ 5:52 am

5. nobody Says:
   April 27th, 2008 at 6:06 am

   Here

   I hope I'm doing this right.

Comment by nobody — April 27, 2008 @ 6:06 am

6. nobody Says:
   April 27th, 2008 at 6:07 am

   Look at that. It worked!

   There you have it. Proof that you CAN teach an old dog new tricks.

   

Comment by nobody — April 27, 2008 @ 6:07 am

7. Zachriel Says:
   April 27th, 2008 at 9:30 am

   AnaxagorasRules: because mitochondrial DNA is similar to that found in bacterial cells, it is thought that mitochondria arose from bacteria that invaded the ancestors of plant and animal cells

   Not only is there genetic homology, but there are also striking structural resemblances between mitrochondria and bacteria. The DNA is circular, unlike nuclear DNA. The mitochondria has more than one membrane, including one that resembles that of bacteria. Their ribosomes match those of bacteria. Mitochondria reproduce by binary fission.

   In modern organisms, mitrochondria are highly integrated with the cell, and many of the genes from the ancient bacterium have apparently migrated to the nucleus.

   AnaxagorasRules: Just how the heck does something the size of a mitochondrion get through a cell's plasma membrane in the first place?

   Like the Grim Reaper"”through the opened door.

   There is a heterotrophic protist that engulfs a free living alga. The alga then losses its cytoskeleton and flagella. The protist becomes autotrophic (via photosynthesis). This process gives us clues as to how this process may have occurred in the distant past.
   Okamoto and Inouye, Science 2005

Comment by Zachriel — April 27, 2008 @ 9:30 am

8. Raevmo Says:
   April 27th, 2008 at 9:52 am

   Bradford:

   When I read things like this I wonder what it would have been like just prior to the advent of mitochondria? If mitochondria are a cell division command center then where was the eukaryotic command center prior to mitochondria or if one says really Bradford, eukaryotic cells became so because of mitochondria, this just raises other questions.

   The study shows that mitochondrial genes can affect cell division in yeast, not that mitochondria are in full control. It has been argued that the relationship between mitochondrial genes and nuclear genes is not entirely cooperative, but that they may be in conflict about what the cell as a whole should do. For example, mitochondria are passed on via the maternal line, not the paternal line (there are very very few exceptions to this rule). This creates a conflict between mitochondrial and nuclear genes over the sex of the offspring. Mitochondria do not "want" to end up in males because males are a dead end for them, since males do not transmit mitochondria to the next generation. Nuclear genes on the other hand prefer a balanced sex ratio. Hence there is a conflict. In many plants there is a condition called male sterility, which is caused by mitochondria (or chloroplasts). These plant produce no pollen, but instead channel more energy into ova. This is to the benefit of mitochindria, since more of them will be transmitted to the next generation. In some plants the nuclear genes "strike back" by blocking the male sterilizing action of mitochindrial genes, thus restoring pollen production. In other words, there is an arms race between nuclear and mitochondrial genes over aspects of reproduction at the level of the individual.

Comment by Raevmo — April 27, 2008 @ 9:52 am

9. Allen_MacNeill Says:
   April 27th, 2008 at 11:04 am

   It's very gratifying to see my old friend, Lynn Margulis, finally getting the recognition that she deserves. As the originator of the serial endosymbiosis theory (SET) for the origin of eukaryotes, Lynn's work provides an excellent example of how ID should (but currently doesn't) proceed. During the late 1960s, Lynn published a series of revolutionary papers on the evolution of eukaryotic cells, culminating in her landmark book Symbiosis and Cell Evolution, in which she carefully laid out the empirical evidence supporting the theory that mitochondria, choloroplasts, and undulapodia (eukaryotic cilia and flagella) were once free living bacteria (purple sulfur bacteria, cyanobacteria, and spirochaetes, respectively).

   Her theory was greeted with contempt and scorn by almost all evolutionary biologists (sound familiar?), who believed at the time that all eukaryotic cellular organelles evolved by gradual elaboration of invaginations of the plasma membrane. But Lynn didn't give up, or continue to simply restate her original theory (sound familiar?). Instead, she continued to do extensive field and laboratory research, publishing hundreds of papers and dozens of books in which she presented the accumulating empirical evidence supporting her theory. With time, other researchers (encouraged by the success of her field and lab research) began to test her hypotheses themselves, and discovered yet more empirical evidence supporting her theory.

   And so today, Lynn Margulis's SET has become the dominant theory explaining not only the origin of eukaryotes, but also the origin of evolutionary novelty at dozens of different levels in biology (see her Acquiring Genomes for a comprehensive review). So well accepted has her work become by evolutionary biologists that finally, after almost four decades, creationists and ID supporters have begun to attack her theories. As she said at our Darwin Day celebration at Cornell this past February, no greater affirmation of one's "having arrived" as a major theorist in evolutionary biology could be imagined.

   The point here is that, if ID wants to become accepted as part of evolutionary biology in the same way that Lynn Margulis's SET has become accepted, then ID supporters have to do the same thing she did: get out in the field and get your hands dirty, and get into the lab and do the same thing. Her ideas were just as unorthodox and unacceptable in 1969 as ID is now. However, she didn't put all of her effort into public relations and political propaganda. No "Symbiosis Institute" dumped millions into the production of deliberately distorted press kits and one-sided propaganda films. Legions of self-appointed experts whose only exposure to biology was in high school classes or what they read on Answers in Genesis or Uncommon Descent bloviated on SET and declared themselves experts after a week of superficial study of articles on Wikipedia.

   No, Lynn and her colleagues did the hard work of finding the empirical evidence that eventually carried the day and established her SET as one of the bedrock foundations now worthy enough of respect as to earn the ire of the creationists and IDers. Her ideas are still radical, and still raise the blood pressure of many evolutionary biologists. Her dismissal of the "modern evolutionary synthesis" in particular is not popular among many evolutionary biologists, who are largely still mired in paradigms that are at least four decades of out of date. She has said some things about the "modern synthesis" that have brought smiles to the faces of the creationist quote-miners. The difference between her and them is that they can't even begin to claim any credibility in science; their "work" is entirely parasitic on hers, and deserves nothing but contempt.

   When the history of evolutionary biology in the 20th century is written (I hope to contribute to it myself, if I live long enough), the work of Lynn Margulis will rank right up there with the work of Fisher, Haldane, Wright, Dobzhansky, Mayr, Simpson, Stebbins, Gould, Lewontin, Kimura, Williams, Hamilton, Trivers, and the two Wilsons. And unless and until IDers decide that it's finally time to stop doing agitprop and start doing science, they and the creationists will at best be a trivial footnote.

Comment by Allen_MacNeill — April 27, 2008 @ 11:04 am

10. Raevmo Says:
    April 27th, 2008 at 11:21 am

    Allen:

    When the history of evolutionary biology in the 20th century is written (I hope to contribute to it myself, if I live long enough), the work of Lynn Margulis will rank right up there with the work of Fisher, Haldane, Wright, Dobzhansky, Mayr, Simpson, Stebbins, Gould, Lewontin, Kimura, Williams, Hamilton, Trivers, and the two Wilsons.

    I almost entirely agree. She deserves the Nobel for her work. I'm not so sure about including D.S. Wilson in that list though, and you forgot John Maynard Smith.

Comment by Raevmo — April 27, 2008 @ 11:21 am

11. MikeGene Says:
    April 27th, 2008 at 11:58 am

    Hi Allen,

    I basically agree with your assessment, but as I explain at TeleoLogic, I think it is more complicated than this.

    Also, you mention:

    Her ideas were just as unorthodox and unacceptable in 1969 as ID is now.

    I don't agree here. Unlike Margulis's ideas, design arguments come with a long history of metaphysical baggage and the current expression (ID) is now linked to socio-political baggage. What's more, as many have argued, ID represents a threat to science itself, as it is argued that acceptance of ID into science would overturn many of the ground rules of science. I don't think anyone seriously viewed Margulis's ideas as a challenge to the way science is done. It was simply a challenge to views about how evolution occurred.

    In other words, if you could show that Margulis's ideas were tied to a long religious tradition, that they called into question the basic ground rules of science, and that a group of activists were trying to get her ideas taught in the schools in order to tap into that long religious tradition, then I think you could legitimately say that "her ideas were just as unorthodox and unacceptable in 1969 as ID is now."

Comment by MikeGene — April 27, 2008 @ 11:58 am

12. AdR Says:
    April 27th, 2008 at 12:04 pm

    And so today, Lynn Margulis's SET has become the dominant theory explaining not only the origin of eukaryotes, but also the origin of evolutionary novelty at dozens of different levels in biology

    Margulis' theory involves all kinds of imaginary organisms that can form hybrids to create almost anything. Her theories are not based on actual mechanistic events and she hops from one organism to the other as if evrything were possible. You need a eukaryote? You just put 2 bacteria together according to Margulis. Is that science, I don't think so. But it makes good fairytales. Maybe she can get the Nobel prize for peace.

Comment by AdR — April 27, 2008 @ 12:04 pm

13. Bradford Says:
    April 27th, 2008 at 12:33 pm

    Hi Raevmo. I read your comment with much interest. I also liked nobody's link. That moniker catches your attention doesn't it? I'm quoting from the paper:

    A protein linked to both metabolism and DNA replication is the Sir2p sirtuin [11], which negatively impacts DNA replication [16]"“[18]. Consequently, we evaluated cell cycle progression of cells lacking Sir2p alone, or in combination with Abf2p over-expression (Figure 4). Comparison of ABF2+, SIR2+ (Figure 4, top row) to ABF2+, sir2Δ (Figure 4, third row) cells at 60 min shows that cells lacking SIR2 initiated and completed S phase significantly sooner than wild type cells. Initiation of DNA replication was further accelerated in 3xABF2+, sir2Δ cells (Figure 4, bottom row).

    I'll explain the bold annotation later but this paragraph emphasizes the replication aspects highlighted in Mike's post. More:

    Sir2p is an evolutionarily conserved NAD+-dependent de-acetylase [10],[11]. Loss of Sir2p leads to loss of transcriptional silencing, genome instability and a decrease in replicative life span. In yeast, silent chromatin is formed at three regions: the rDNA, the HML and HMR mating type loci, and telomeres [12]. Sir2p is required for silencing at all of these regions, and it is the only Sir protein required for silencing at the rDNA [13]"“[15]. Sir2p also appears to negatively impact on rDNA replication, because in sir2Δ cells twice as many origins are activated within the rDNA array [16]. The inhibitory effects of Sir2p on DNA replication extend beyond rDNA. Loss of Sir2p suppresses replication defects of mutants that cannot assemble a pre-replicative complex of proteins (pre-RC) at origins of DNA replication in the G1 phase of the cell cycle [17]. These results may be linked to a general positive role of histone acetylation for origin activity [18]. Indeed, loss of the Rpd3p de-acetylase globally accelerated DNA replication, and targeted acetylation of a late origin advanced its activation [19], demonstrating a clear causal role of histone acetylation and activation of DNA replication. However, whether such chromatin modifications may serve as a link between cellular metabolism and initiation of DNA replication is not known.

    This points to elaborate regulatory mechanisms controlling the replication of DNA leading to this:

    In this report we show that an increase in mtDNA in cells over-expressing Abf2p, actively promotes initiation of cell division. Furthermore, we identify physical changes, such as Sir2p binding and histone acetylation, at an origin of DNA replication that result from an increase in mtDNA.

    Note the interactive nature of cellular functions involving mitochondrial DNA. How does this look to you- cooperative or competitive with respect to mitochondria and nuclear DNA? More:

    We hypothesized that increasing the amount of mtDNA may mimic the situation of "evolved" yeast populations, which can proliferate faster than the parent population [2], allowing us to examine effects on cell division… These data suggest a connection between mitochondrial function and cell cycle progression that is evident under glucose limitation in cells over-expressing ABF2. Interestingly, 3xABF2+ cells are the same size as wild type cells (Figure 2A), possibly explaining why ABF2 mutations were not identified previously in size-based mutant screens for cell cycle regulators.

    More regulatory responses to environmental factors involving mitochondrial DNA. And this little blurb:

    mtDNA abundance is not increased in cells lacking Sir2p.

    Which came first in an evolutionary timeline- mitochondrial DNA or Sir2p? I see possibilities for a front loading perspective.

Comment by Bradford — April 27, 2008 @ 12:33 pm

14. Raevmo Says:
    April 27th, 2008 at 12:42 pm

    AdR:

    You need a eukaryote? You just put 2 bacteria together according to Margulis.

    I guess you don't really expect us to believe that Margulis' reasoning is that simplistic. Do you think that she is not aware of the fact that bacteria can live inside other bacteria without forming a eukaryote? (von Dohlen et al. 2001, Nature 412).

Comment by Raevmo — April 27, 2008 @ 12:42 pm

15. Bradford Says:
    April 27th, 2008 at 12:48 pm

    Raevmo: I guess you don't really expect us to believe that Margulis' reasoning is that simplistic. Do you think that she is not aware of the fact that bacteria can live inside other bacteria without forming a eukaryote? (von Dohlen et al. 2001, Nature 412).

    Understood but I'm reminded of a comment made by David Berlinski when I read this. He spoke of a lack of conceptual clarity related to explanations like this and compared such evolutionary scenarios unfavorably to physics and mathematics. Precision and clarity being greatest with mathematics, a little less so for physics and much less so for evolutionary biology.

Comment by Bradford — April 27, 2008 @ 12:48 pm

16. Raevmo Says:
    April 27th, 2008 at 1:17 pm

    Bradford:

    Understood but I'm reminded of a comment made by David Berlinski when I read this. He spoke of a lack of conceptual clarity related to explanations like this and compared such evolutionary scenarios unfavorably to physics and mathematics. Precision and clarity being greatest with mathematics, a little less so for physics and much less so for evolutionary biology.

    Berlinksi is a non-entity in science and mathematics. His publications have zero impact (4 citations in 40 years). So excuse me for not being impressed. But you do realize that biology deals with systems that are a bit more complex than the typical systems physicists work with. That does tend to impinge on clarity and precision.

Comment by Raevmo — April 27, 2008 @ 1:17 pm

17. AdR Says:
    April 27th, 2008 at 1:42 pm

    Raevmo: I guess you don't really expect us to believe that Margulis' reasoning is that simplistic. Do you think that she is not aware of the fact that bacteria can live inside other bacteria without forming a eukaryote? (von Dohlen et al. 2001, Nature 412).

    So, the fact that bacteria can live inside of each other would be proof that a eukaryote has evolved from this? The amount of rework that needs to be done to make a eukaryotic cell out of two prokaryotes is staggering. If you just ignore those steps, i.e. its evolution, it is a 'just so' story with no evolutionary substance.

    If you look at the article about the origin of the eukaryotic cell, Fig. 1 and Fig. 2 you will see that it is nothing more than fantasizing about an imaginary world where we don't have to bother about evolutionary reality: what mechanistic steps were taken and whether they realistic.

    But it is funny in a way, Margulis thinks about evolution as if a Designer would have pieced all the things together with his almighty toolbox.

Comment by AdR — April 27, 2008 @ 1:42 pm

18. Jean Says:
    April 27th, 2008 at 1:49 pm

    Berlinksi is a non-entity in science and mathematics.

    So what is your citation rate, Raevmo?

Comment by Jean — April 27, 2008 @ 1:49 pm

19. Bradford Says:
    April 27th, 2008 at 2:09 pm

    Raevmo:

    Berlinksi is a non-entity in science and mathematics. His publications have zero impact (4 citations in 40 years).

    This ad hom response illustrates the value of Expelled: No Intelligence Allowed. I never see an evolutionary biologist slimed like this and it is not because they are all stellar performers.

    So excuse me for not being impressed.

    The point of the reference was not Berlinksi. I referred to him out of respect for source material. The point is always what is said. I take every commenter at TT seriously. A HS dropout has the capacity for rational thought and may come out with a gem. Obviously a PhD is more likely to have insight into technical details but intellectual snobbery is a bore and a sign of insecurity.

Comment by Bradford — April 27, 2008 @ 2:09 pm

20. Raevmo Says:
    April 27th, 2008 at 2:13 pm

    Fair enough, I shouldn't have said that.

Comment by Raevmo — April 27, 2008 @ 2:13 pm

21. Raevmo Says:
    April 27th, 2008 at 3:06 pm

    AdR:

    So, the fact that bacteria can live inside of each other would be proof that a eukaryote has evolved from this?

    No, it proves that bacteria can stably live inside each other. This increases the plausibility of Margulis' scenario, does it not?

    The amount of rework that needs to be done to make a eukaryotic cell out of two prokaryotes is staggering.

    I guess you are talking about contemporary prokaryotes and eukaryotes. Sure, that would take a billion years of evolution. Oh, wait.

Comment by Raevmo — April 27, 2008 @ 3:06 pm

22. olegt Says:
    April 27th, 2008 at 3:21 pm

    Bradford wrote:

    The point of the reference was not Berlinksi. I referred to him out of respect for source material. The point is always what is said. I take every commenter at TT seriously. A HS dropout has the capacity for rational thought and may come out with a gem. Obviously a PhD is more likely to have insight into technical details but intellectual snobbery is a bore and a sign of insecurity.

    Exactly, Bradford. Tell me, though, why do creationists proudly wear their degrees on a sleeve? Like Dr. Dr. Dembski and Dr. Dr. Wells?

Comment by olegt — April 27, 2008 @ 3:21 pm

23. Bilbo Says:
    April 27th, 2008 at 4:33 pm

    AdR:

    But it is funny in a way, Margulis thinks about evolution as if a Designer would have pieced all the things together with his almighty toolbox.

    Yes, that's what occurred to me when I read her book, Acquiring Genomes. It's almost as if there were pre-designed modular units meant to combine with each other to form more complex units. I didn't know creationists or IDists were attacking her ideas, Allen. If they thought about front-loaded evolution, they might find her helpful.

Comment by Bilbo — April 27, 2008 @ 4:33 pm

24. AnaxagorasRules Says:
    April 27th, 2008 at 4:45 pm

    Hi, Zachriel,

    Not only is there genetic homology, but there are also striking structural resemblances between mitrochondria and bacteria. The DNA is circular, unlike nuclear DNA.

    1. If mitochondria arose from invading bacteria, then why are there still structuaral resemblances, given the different environments and the time apart?

    2. Assuming that prior to the invasion that some other part of the cell was involved in cell respiration, where is that remnant?

Comment by AnaxagorasRules — April 27, 2008 @ 4:45 pm

25. Zachriel Says:
    April 27th, 2008 at 8:37 pm

    AnaxagorasRules: 1. If mitochondria arose from invading bacteria, then why are there still structuaral resemblances, given the different environments and the time apart?

    Evolution works by adapting existing structures, but that doesn't mean that every aspect of the structure will disappear over time. The purpose of the endosymbiotic relationship is to acquire the advantages of each partner while dispensing with the overlap and optimizing the integration (much like a corporate merger).

    For instance, the inner membrane of the mitochondria is highly adapted with infoldings (cristae) to increase the available surface area, but still recognizable as 'foreign', having many features (e.g. certain lipids) found only in bacteria, but nowhere else in the cell. The other membrane more closely resembles a phagocytosis membrane, harking back to the origin of the relationship. (There may be other membranes, as well.)

    There are several lines of evidence that fit with the hypothesis of endosymbiosis. But there is still a lot to learn. There was probably a great deal of horizontal evolution in the early history of life.

    AnaxagorasRules: 2. Assuming that prior to the invasion that some other part of the cell was involved in cell respiration, where is that remnant?

    Still there. Glycolysis occurs in the cytoplasm, and as it is a metabolic pathway available to virtually all organisms, presumably preceded respiration. (Fermentation, on the other hand, is probably due to a bacterial endosymbiont.)

Comment by Zachriel — April 27, 2008 @ 8:37 pm

26. JackT Says:
    April 28th, 2008 at 1:21 am

    Mike,

    Where do you see yourself in ten years? Will you still be wagging your finger at Dawkins and PZ Myers? Posting rabbit pictures? Jiggling scientific articles until they vibrate to the tune of intelligent design? When are you going to be the author of one of those scientific articles? Will you buckle down and get your hands dirty, as Allen mentioned? Or do plan to keep blogging from the sidelines?

    I don't mean this to sound disrespectful. I am just curious what you hope to accomplish?

Comment by JackT — April 28, 2008 @ 1:21 am

27. kornbelt888 Says:
    April 28th, 2008 at 9:40 am

    JackT,

    Whatever he's doing, I'll bet you'll be reading it.

Comment by kornbelt888 — April 28, 2008 @ 9:40 am

28. Nick Says:
    April 28th, 2008 at 9:51 am

    AnaxagorasRules:
    In fact, it sounds like a bunch of whacked out BS. Just how the heck does something the size of a mitochondrion get through a cell's plasma membrane in the first place? Protiens and solutes and ions get through the membrane, not entire organisms, for crying out loud! Unless bacteria have some sort of magical open sesame key. Of course, I'm no bacteria expert.

    Well, I guess knowing that you are clueless is a first step, but don't you think it would be good to have some basic familiarity with the topic before declaring Margulis's research "whacked out BS?" It makes you sound kind of shrill.

    There are many bacteria that are capable of getting through a cell's plasma membrane, and I really don't think it requires magic. Some are beneficial symbionts. Others are pathogenic. I'm sure you have heard of some of them: Salmonella, Shigella, Yersinia, Listeria.

    Check out this link http://www.jci.org/articles/vi...
    Cossart, P. (1997). Subversion of the Mammalian Cell Cytoskeleton by Invasive Bacteria. Journal of Clinical Investigation 99:2307.

    I'm no bacteria expert either, but the google search took less than one minute.

Comment by Nick — April 28, 2008 @ 9:51 am

29. Bradford Says:
    April 28th, 2008 at 11:59 am

    JackT: Will you still be wagging your finger at Dawkins and PZ Myers?

    It's interesting that the Jack Ts of the world do not pose the same questions to the likes of Dawkins and Myers. Most of what is posted at their sites is not science related. It is more socio-political in substance and tone. Their followers understand the significance of this and have no need of inquiring as to what these men wish to accomplish. The goals are a given.

Comment by Bradford — April 28, 2008 @ 11:59 am

30. olegt Says:
    April 28th, 2008 at 12:33 pm

    Bradford wrote:

    It's interesting that the Jack Ts of the world do not pose the same questions to the likes of Dawkins and Myers. Most of what is posted at their sites is not science related. It is more socio-political in substance and tone. Their followers understand the significance of this and have no need of inquiring as to what these men wish to accomplish. The goals are a given.

    Good point, Bradford. Dawkins and Myers are no longer conducting research, they are teachers and popularizers of science. However, mainstream biology has lots of researchers and that's where the difference with ID lies. So far all IDers have been popularizers of ID. There is no ID research to speak of. JackT's question should be seen in that larger context.

Comment by olegt — April 28, 2008 @ 12:33 pm

31. Bradford Says:
    April 28th, 2008 at 12:58 pm

    olegt: Good point, Bradford. Dawkins and Myers are no longer conducting research, they are teachers and popularizers of science.

    Popularizers of their own philosophical perspectives would be a more accurate description.

    However, mainstream biology has lots of researchers and that's where the difference with ID lies. So far all IDers have been popularizers of ID. There is no ID research to speak of. JackT's question should be seen in that larger context.

    Fair enough. There is a body of work needed before ID could be considered a scientific discipline. That point is not an issue at TT. You do overstate your case though if you think there is no ID related research.

    Axe DD (2000) Extreme functional sensitivity to conservative amino acid changes on enzyme exteriors. Journal of Molecular Biology 301: 585-595. PMID: 10966772

    von Sternberg R (2000) Genomes and form. The case for teleomorphic recursivity. Annals of the New York Academy of Sciences 901: 224-236. PMID: 10818573

    Axe DD, Foster NW, Fersht AR (1998) A search for single substitutions that eliminate enzymatic function in a bacterial ribonuclease. Biochemistry 37: 7157-7166. PMID: 9585527

    Axe DD, Foster NW, Fersht AR (1996) Active barnase variants with completely random hydrophobic cores. Proceedings of the National Academy of Sciences USA. 93: 5590-5594. PMID: 8643620

Comment by Bradford — April 28, 2008 @ 12:58 pm

32. olegt Says:
    April 28th, 2008 at 1:09 pm

    Hi Bradford,

    You do overstate your case though if you think there is no ID related research.

    What is the difference between ID-related research and pure ID research?

Comment by olegt — April 28, 2008 @ 1:09 pm

33. AnaxagorasRules Says:
    April 28th, 2008 at 1:33 pm

    Hi, Nick,

    Well, I guess knowing that you are clueless is a first step, but don't you think it would be good to have some basic familiarity with the topic before declaring Margulis's research "whacked out BS?" It makes you sound kind of shrill.

    If I think something is BS, then that's the way I'll phrase it. If I think something sounds like BS, then that's the way I'll phrase it. There is a difference in the semantics. I realized that I could be wrong. That's why I added the phrase that I was not an expert, which implies uncertainty. Not because I thought someone might think I was an expert, but because I wanted to strongly imply the uncertainty under which my comment was made. I was under no illusion that my comment would stand if it were the case that I was wrong, and I was cognizant of the fact that I could be wrong. Thanks for the link.

Comment by AnaxagorasRules — April 28, 2008 @ 1:33 pm

34. Bradford Says:
    April 28th, 2008 at 2:18 pm

    olegt: What is the difference between ID-related research and pure ID research?

    I could ask the same question about research in general. A very small percentage of it is done with an origins perspective as the core hypothesis. We are likely to see a descriptive phrase like evolutionary conserved in the midst of a paper depicting results of an investigation into a biological function having medical implications and correct in believing the observation was incidental to the main thrust of the paper. Research is value neutral. Any research can lead to data favoring any particular theory even if that was not the researcher's intent.

Comment by Bradford — April 28, 2008 @ 2:18 pm

35. Doug Says:
    April 28th, 2008 at 3:01 pm

    JackT said:

    Where do you see yourself in ten years? Will you still be wagging your finger at Dawkins and PZ Myers? Posting rabbit pictures? Jiggling scientific articles until they vibrate to the tune of intelligent design? When are you going to be the author of one of those scientific articles? Will you buckle down and get your hands dirty, as Allen mentioned? Or do plan to keep blogging from the sidelines?

    I just like how JackT initially comes to this board under the guise of an interested, open-minded chap not too concerned about the rhetorical games being played on both sides.
    Give him a bit of time and the veneer falls off.

    I don't mean this to sound disrespectful.

    LOL. Sure.

    I am just curious what you hope to accomplish?

    BwwwaaHAHAHAHA
    "I'm just so genuinely curious that I'm going to describe your position in one of the more derisive ways my mind can whip together."

Comment by Doug — April 28, 2008 @ 3:01 pm

36. nobody Says:
    April 28th, 2008 at 7:25 pm

    Is there a delete key on this board?

    Just curious.

Comment by nobody — April 28, 2008 @ 7:25 pm

37. Joy Says:
    April 28th, 2008 at 8:38 pm

    Hi, nobe. For an amount of time there is an "edit this" blue link right after the date and time link under your name. You can delete your post from that function.

    Contributors have edit function on all posts all the time, but by mutual agreement we don't edit or delete other people's posts (not even troll posts). Trolls, off-topic and some insult comments get sent to the Memory Hole - our vast wasteland of dreck - and we have a nice new feature that allows us to ban a user from posting to a thread. By mutual agreement we don't moderate other contributor's threads, just our own.

Comment by Joy — April 28, 2008 @ 8:38 pm

38. JackT Says:
    April 28th, 2008 at 9:34 pm

    Nonetheless it is a legitimate question to ask what the ultimate goal of blogging is, if there is one. Attempts to assail the questioner will not make the question go away.

    Given the formula of (1) opinionating about other people's opinions, (2) rabbit pictures, and (3) citing scientific papers with hand-waiving arguments in favor of ID, I cannot see how the cause of ID will be advanced.

    But maybe it's just for fun, I don't know.

Comment by JackT — April 28, 2008 @ 9:34 pm

39. MikeGene Says:
    April 28th, 2008 at 10:32 pm

    Hi Jack T,

    Where do you see yourself in ten years? Will you still be wagging your finger at Dawkins and PZ Myers? Posting rabbit pictures? Jiggling scientific articles until they vibrate to the tune of intelligent design? When are you going to be the author of one of those scientific articles? Will you buckle down and get your hands dirty, as Allen mentioned? Or do plan to keep blogging from the sidelines?

    I don't mean this to sound disrespectful. I am just curious what you hope to accomplish?

    LOL. If you didn't mean to sound disrespectful, and were simply curious, then you would have simply asked, "Mike, I'm curious, where do you see yourself in ten years?" In that case, you wouldn't have had to add, "I don't mean to sound disrespectful." So now I'm curious about something. If you were simply curious, and meant no disrespect, why the need for the additional six editorial statements reframed as questions?

Comment by MikeGene — April 28, 2008 @ 10:32 pm

40. JackT Says:
    April 29th, 2008 at 12:01 am

    Mike,

    Direct questioning is often interpreted as a form of disrespect. Children engage in direct questioning until they (very sadly) learn the social taboo against it. The taboo is invented by adults, who do not appreciate their views being questioned.

    That being the case, the "no disrespect" line is a fairly effective way to circumvent the taboo. It encourages the listener to focus on the question rather than becoming sidetracked by the feeling of disrespect caused by the question. That feeling is a social construction anyway, which acts in concert with the taboo.

    You said my questions are editorial. They are a statement of my current perception of this blog, however you wish to call it. The questions certainly are direct, and they constitute a challenge. They are from an outsider who is asking sincerely.

    So, pretend my questions came from a little kid. There! I just gave you some rhetorical lunch meat. What is your answer?

Comment by JackT — April 29, 2008 @ 12:01 am

41. MikeGene Says:
    April 29th, 2008 at 12:52 am

    Hi JackT,

    Direct questioning is often interpreted as a form of disrespect. Children engage in direct questioning until they (very sadly) learn the social taboo against it. The taboo is invented by adults, who do not appreciate their views being questioned.

    That being the case, the "no disrespect" line is a fairly effective way to circumvent the taboo. It encourages the listener to focus on the question rather than becoming sidetracked by the feeling of disrespect caused by the question. That feeling is a social construction anyway, which acts in concert with the taboo.

    Hmmm. So let me get this straight.

    According to you, this is disrespect:

    "Mike, I'm curious, where do you see yourself in ten years?"

    But this is not disrespect:

    Where do you see yourself in ten years? Will you still be wagging your finger at Dawkins and PZ Myers? Posting rabbit pictures? Jiggling scientific articles until they vibrate to the tune of intelligent design? When are you going to be the author of one of those scientific articles? Will you buckle down and get your hands dirty, as Allen mentioned? Or do plan to keep blogging from the sidelines?

    I don't mean this to sound disrespectful. I am just curious what you hope to accomplish?

    LOL. But hey, it's late and I'm dead tired. Perhaps others can offer some feedback.

    In the meantime, do you think your questions are important? Mind you, I don't mind answering them, but I post mostly late at night during the week. And since they don't look like important questions to me, can you wait until the weekend? I'm off to get some zzzzzs.

Comment by MikeGene — April 29, 2008 @ 12:52 am

42. Wonders For Oyarsa Says:
    April 29th, 2008 at 1:01 am

    Hi JackT,

    My, you are a wee bit pretentious. Standards of politeness and civility a social construct? Indeed they are, and a good thing too! So is the English language. If you want to communicate effectively, I suggest you employ them to that end - rather than being rude and then wishing the rest of the world would get over its socially conditioned aversion to rudeness.

    A simple apology to Mike would be a good start. Try it - you'll feel a socially conditioned sense of being a more mature person because of it.

    P. S. - I hope you die.

    P. P. S. - It's a shame that people have socially conditioned ideas that when people say "I hope you die" they mean something negative, rather than an invitation to a tea party. That's what I mean when I say it.

    P. P. P. S. - Then again, perhaps by "tea party" I mean flaming pit of lava…I never was one for socially conditioned standards for the meaning of words.

Comment by Wonders For Oyarsa — April 29, 2008 @ 1:01 am

43. JackT Says:
    April 29th, 2008 at 1:53 am

    Mike: According to you, this is disrespect: [...] But this is not disrespect: [...]

    This is coming out of left field. I did not demarcate one from the other.

    Oyarsa: Standards of politeness and civility a social construct?

    Also out of left field; a strawman.

    Nevertheless it is certainly true that taboos are constructed around uncomfortable questions. The taboos serve to avoid the questions quite effectively by pointing a finger at the questioner.

Comment by JackT — April 29, 2008 @ 1:53 am

44. Joy Says:
    April 29th, 2008 at 10:00 am

    Mike to Jack:

    LOL. But hey, it's late and I'm dead tired. Perhaps others can offer some feedback.

    Slow recovery rate here, from weekend over-doing (and a serious Irish wake that last I heard, is still going…). But I'll give it a try.

    With all due respect Jack, nobody is fooled by your pretense on this line of questioning (in more than one thread). For instance, pretending you have no idea why people blog, or what blogging is supposed to be. Your pointed questions to a single blogger on this blog with 14 enabled contributors.

    You are not the first ID critic / DarwinDefender to attempt to pin Mike Gene on specifics in hopes of discovering his secret identity. We've been down this road a few times through the years, and it's always people who insist that the kind of professional harassment, character assassination and job discrimination described in the movie Expelled simply does not happen who engage this sort of garbage.

    My extrapolation from observations is that this sort of garbage has an "ultimate goal" too. Should Mike Gene turn out to actually be a real biologist, the professional harassment, character assassination and job discrimination DDs are so famous for can be employed against him as a dangerous threat to Almighty Science. SOP - Standard Operating Procedure.

    Because we are so familiar with the M.O., you're probably not going to succeed in the quest (thereby ingratiating yourself with the inner cadre of DDs who are so obsessed with Mike Gene's secret identity). If you are not interested in the subject matter or slant of this blog, you can easily go elsewhere and do something you are more interested in doing. We won't miss you.

    As for what this blog is, read the line of type below the blue banner at the top of the page. It says: Telic Thoughts is an independent blog about intelligent design. If you have trouble parsing that sentence, you probably won't understand much else here, since we use computers - and typed words - to communicate. You could probably find a pastime that doesn't require you to interpret written words.

Comment by Joy — April 29, 2008 @ 10:00 am

45. nobody Says:
    April 29th, 2008 at 11:22 am

    Dear Mike,

    I don't mean this to sound disprespectful, if you know what I mean. I am just curious about one thing. Why are there are no pictures of coyotes on this blog?

    

Comment by nobody — April 29, 2008 @ 11:22 am

46. Bradford Says:
    April 29th, 2008 at 12:11 pm

    Nobody, you are a wily one.

Comment by Bradford — April 29, 2008 @ 12:11 pm

47. Bilbo Says:
    April 29th, 2008 at 7:03 pm

    Jack T.,

    Where do you see yourself in 10 years? Still asking irrelevant questions at Telicthoughts? Still refusing to read Mike Gene's books? Still demanding positive evidence for ID, but never asking yourself what would constitute positive evidence? In other words, still never really contributing to either side in the debate? Still being a useless, tiresome sot?

    Disrespect fully intended.

Comment by Bilbo — April 29, 2008 @ 7:03 pm

48. MikeGene Says:
    April 29th, 2008 at 7:08 pm

    Hi Nobody,

    I don't mean any disrespect, but there was.

Comment by MikeGene — April 29, 2008 @ 7:08 pm

49. MikeGene Says:
    April 29th, 2008 at 7:10 pm

    Hi JackT,

    This is coming out of left field. I did not demarcate one from the other.

    Then you didn't answer my orginal question.

    Come to think of it, you didn't anwer my other question either.

Comment by MikeGene — April 29, 2008 @ 7:10 pm

50. JackT Says:
    April 29th, 2008 at 8:30 pm

    Joy: You are not the first ID critic / DarwinDefender to attempt to pin Mike Gene on specifics in hopes of discovering his secret identity.

    From beginning to end, this post is pure conspiratorial fantasy. For example, above, how did you arrive at the conclusion that my real motive is to discover MikeGene's "secret identity" I wonder if this is a joke?

Comment by JackT — April 29, 2008 @ 8:30 pm

51. JackT Says:
    April 29th, 2008 at 8:38 pm

    Mike: Then you didn't answer my orginal question.

    Come to think of it, you didn't anwer my other question either.

    Oh? I thought I did. Could you be more specific? In any case, you have still not answered the first questions posed to you, remarking "I'm off to get some zzzzzs," so you were already behind in the answering-tally when you wrote the above.

Comment by JackT — April 29, 2008 @ 8:38 pm

52. Bradford Says:
    April 29th, 2008 at 10:58 pm

    JackT: In any case, you have still not answered the first questions posed to you, remarking "I'm off to get some zzzzzs," so you were already behind in the answering-tally when you wrote the above.

    Jack, where do you see yourself in ten years if he doesn't respond within that time frame?

Comment by Bradford — April 29, 2008 @ 10:58 pm

53. MikeGene Says:
    April 29th, 2008 at 11:47 pm

    Hi JackT,

    As another demonstration of my willingness to walk that extra mile, instead of getting needed zzzzzs, here are my responses ahead of schedule.

    Where do you see yourself in ten years?

    I don't know. I'm not the type who plans his life with ten-year action plans. In fact, ten years ago I would not have guessed that I would be where I now am. It doesn't even make too much sense to focus on ten years out since none of us know that we will even be here ten years from now. So I try, as much as I can, to take one day at a time.

    Will you still be wagging your finger at Dawkins and PZ Myers?

    Maybe. Maybe not. It depends on a)whether I am still blogging; b) whether they are still making claims deserving of criticism and analysis; and c) whether I notice them and feel like offering a critique.

    Posting rabbit pictures?

    Why not? Do you have something against rabbits? Come now, you'd have to be one cold-hearted person not to have your day a tad bit lightened by this little guy:

    

    Jiggling scientific articles until they vibrate to the tune of intelligent design?

    Probably, since the stack continues to grow. What's so fascinating (to me, at least) is that all it takes is some gentle jiggling and the rabbit pokes his head out. This is because so much of molecular, cell, and evolutionary biology has become quite friendly (unintentionally so) to a teleological perspective and I expect this trend to continue. So why wouldn't I maintain such an interest?

    When are you going to be the author of one of those scientific articles?

    You are back to criticizing something that is not science for not being science. How can I be the author of a scientific article about ID if ID is not science? You need to get it through your head (no disrespect intended) that ID is not science.

    Look at it this way. I don't know about you, but I think the results section of a scientific article is more important than the list of authors. As such, results are data and data are always open to reinterpretation by anyone.

    Will you buckle down and get your hands dirty, as Allen mentioned? Or do plan to keep blogging from the sidelines?

    Since I am not a glory-hound, I have no problem with making observations from the sidelines. I have no problem with letting science be science and allowing mainstream views employ a non-teleological perspective to interpret and explain the data. We thus get to see the mainstream non-teleological explanation at its best. It's just that some of us on the sidelines simply note that such interpretations are often not necessary here on the sidelines. Thankfully, we still live in a free country where we can share our observations and impressions with each other without having to bow to authority.

    I don't mean this to sound disrespectful. I am just curious what you hope to accomplish?

    I've explained this before. This is a topic that has been debated in Western civilization for over 2000 years. And TT is a semi-popular blog that deals with what is now an extremely contentious issue. It draws comments and emotions from people at both ends of the spectrum. Our goal is to create at least one place on the internet where such discussions can be had while minimizing all the chest-thumping and hostility that is commonplace in this debate. Are we perfect? Of course not; we're human. But do you know of a better blog that seeks the same goal?

    If, for some strange reason, you are troubled by this blog, or me, there is a very simple solution "“ stop reading.

Comment by MikeGene — April 29, 2008 @ 11:47 pm

54. MikeGene Says:
    April 30th, 2008 at 10:00 pm

    Allen: Her ideas were just as unorthodox and unacceptable in 1969 as ID is now.

    My rebuttal:

    I don't agree here. Unlike Margulis's ideas, design arguments come with a long history of metaphysical baggage and the current expression (ID) is now linked to socio-political baggage. What's more, as many have argued, ID represents a threat to science itself, as it is argued that acceptance of ID into science would overturn many of the ground rules of science. I don't think anyone seriously viewed Margulis's ideas as a challenge to the way science is done. It was simply a challenge to views about how evolution occurred.

    In other words, if you could show that Margulis's ideas were tied to a long religious tradition, that they called into question the basic ground rules of science, and that a group of activists were trying to get her ideas taught in the schools in order to tap into that long religious tradition, then I think you could legitimately say that "her ideas were just as unorthodox and unacceptable in 1969 as ID is now."

    Now, for some perfect timing. I give you PZ Myers:

    Hah! In my recent debate with Angus Menuge (I keep meaning to write it up, but every time I recall that evening I fall asleep), I pointed out that one of the goals of the ID movement was to redefine science; he agreed, but said that what they wanted to do was restore the true meaning of science, to that of "¦ Aristotle. I had to reply that apparently, then, they wanted to roll back progress by 25 centuries.

    Can anyone find evidence that Margulis's critics accused her of wanting to redefine science itself, with Margulis herself agreeing?

Comment by MikeGene — April 30, 2008 @ 10:00 pm

55. MikeGene Says:
    May 2nd, 2008 at 7:26 am

    Thought not.

Comment by MikeGene — May 2, 2008 @ 7:26 am

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