The Summer of Front-loading

It was a fun and productive summer:

1. I provided evidence to support the hypothesis that the origin of mitochondria was front-loaded and, in doing so, ran across a striking example of molecular convergence.  All of this helps us see how front-loading can guide the blind watchmaker.

How to Guide the Blind Watchmaker

Guiding the Blind Watchmaker again

More Evidence of Front-loading Mitochondria


2. I outlined some evidence showing it to be plausible that blood was front-loaded into single-celled life forms.

Front-loading Blood

3. I outlined a search for the last universal common ancestor of all life

The Hunt for LUCA

and provided evidence that this ancestral state was not much different from a modern day cell:

Protein Domains in LUCA

Genomes and LUCA

4. The hypothesis of front-loading led me to consider the ribosome as a vehicle for front-loading, which in turn, led me to successfully expect:

a. ribosomal proteins would have functions apart from protein translation:

Front-loading with ribosomes

Another Ribosomal Protein Moonlights

b. rRNA would actually code for protein sequence:

Buried Code

c. Permutations of ribosomal protein code would actually code for other proteins:

Digging Up More Buried Code with Ribosomal Protein S5

Using the Ribosome to Encode a Brain Protein

5. I provided more evidence that the genetic code is remarkably exceptional:

An Exceedingly Exceptional Code

6. I provided an example where the choice of amino acids helps to front-load life:

Melanin


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66 responses to “The Summer of Front-loading

  1. I see no evidence for front-loading

  2. I do see evidence of front-loading, duck rabbit 🙂

  3. Thats going to give me nightmares

  4. (Following up guts’ link to this site)

    Point of information, an ISP check should clarify that the first post is not from me. On the other hand, I don’t see any evidence for front loading either.

  5. Alan is correct. The first ‘Alan Fox’ is an imposter.

  6. Not a fan of pre-moderation.

    Nelson directed me here to find scientific evidence for front-loading. Now I am banned at Telic Thoughts, although comments are still being directed to my empty chair.

    Do you honestly believe there is any scientific merit in ID?

    Do you have something that might dent my scepticism?

  7. Oh apologies, I see the comment has gone straight through.

  8. Hi Alan,

    Do you honestly believe there is any scientific merit in ID?

    You would have to define what you mean by “scientific merit?”

    Do you have something that might dent my scepticism?

    It depends if your skepticism is rooted in an open- and fair-minded approach that is sensitive to clues or if it is rooted in a closed-minded approach that demands something extraordinary and shocking. I myself am skeptical of my own views, having admitted there is a good chance I could be wrong about it all. But I obviously don’t consider my own views to be nonsense.

  9. Science deals with reality. Real thing are anything that exists/did exist/will exist in the past and future light cone of the here and now. For something to have scientific merit, such as an alternative hypothesis to ToE, it would need to be grounded in reality. Otherwise it is not scientific.

  10. It depends if your skepticism is rooted in an open- and fair-minded approach that is sensitive to clues or if it is rooted in a closed-minded approach that demands something extraordinary and shocking.

    It’s impossible to predict whether any evidence is convincing before it is presented. Guts seemed quite convinced there was evidence of ID (or at least front loading) to be found here. Is there one particular example that you find telling?

  11. Science deals with reality. Real thing are anything that exists/did exist/will exist in the past and future light cone of the here and now. For something to have scientific merit, such as an alternative hypothesis to ToE, it would need to be grounded in reality. Otherwise it is not scientific.

    That’s hand-waving. There are realities that science cannot deal with. And there are ways to deal with reality that are not science. Are you confusing science with scientism?

    We need to establish first things first. Say, for the sake of argument, that life was indeed designed and thus evolution was front-loaded. Is there any reason to think science could discover this possible reality?

    It’s impossible to predict whether any evidence is convincing before it is presented. Guts seemed quite convinced there was evidence of ID (or at least front loading) to be found here. Is there one particular example that you find telling?

    It is not impossible to predict whether any evidence is convincing before it is presented. Take one particular example of evidence for evolution and go present it on a creationist forum. I predict the creationists will not find it convincing.

    You need to address the point that I raised – It depends if your skepticism is rooted in an open- and fair-minded approach that is sensitive to clues or if it is rooted in a closed-minded approach that demands something extraordinary and shocking.

    I see no evidence that your skepticism is rooted in an open- and fair-minded approach that is sensitive to clues. There is evidence that your skepticism is rooted in a closed-minded approach that demands something extraordinary and shocking.

  12. That’s hand-waving.

    No, it was my poor but honest attempt at answering your question “define scientific merit”. And I do think that science is defined by reality and vice versa. I do not think there is any reality that is not amenable to scientific study.

    We need to establish first things first. Say, for the sake of argument, that life was indeed designed and thus evolution was front-loaded. Is there any reason to think science could discover this possible reality?

    If you mean God created the universe and arranged things so that life arose on Earth resulting in us being in the here and now, I’m not sure. I guess there’s nothing to prevent God from making it clear to us how and why He did things if He wished.

    As to questioning my scepticism, I can’t really see how you can form an opinion on a few comments on your blog.

    As I said, Nelson linked me here claiming I would find evidence for front loading. If he was mistaken, no problem, I’ll stop bothering you.

  13. As to questioning my scepticism, I can’t really see how you can form an opinion on a few comments on your blog. ..As I said, Nelson linked me here claiming I would find evidence for front loading. If he was mistaken, no problem, I’ll stop bothering you.

    Just providing some context .

  14. No, it was my poor but honest attempt at answering your question “define scientific merit”. And I do think that science is defined by reality and vice versa. I do not think there is any reality that is not amenable to scientific study.

    Much of a reality is not amenable to scientific study. If you disagree, perhaps you can explain why we don’t simply replace courtrooms and juries with scientists and labs.

    Or look at it this way. You came to this blog making a claim about reality: “Point of information, an ISP check should clarify that the first post is not from me.”

    So I checked the IPs and they were indeed different, leading me to confirm your claim about reality. Are you saying I used science to confirm your claim about reality and thus made a scientific discovery?

    Then again, it is possible for people to post using more than one IP. So it is possible that you were lying and did indeed post the first comment from ‘Alan Fox.’ How would science determine that you were not lying?

    If you mean God created the universe and arranged things so that life arose on Earth resulting in us being in the here and now, I’m not sure. I guess there’s nothing to prevent God from making it clear to us how and why He did things if He wished.

    No, I did not ask a question about God and theology. And yes, you have evaded yet another question.

    As to questioning my scepticism, I can’t really see how you can form an opinion on a few comments on your blog.

    It’s about evidence, Alan. As I noted, “I see no evidence that your skepticism is rooted in an open- and fair-minded approach that is sensitive to clues.” You have failed to provide any evidence to indicate I am wrong. Do you expect me to embrace opinions without evidence, Alan?

    I also noted, “There is evidence that your skepticism is rooted in a closed-minded approach that demands something extraordinary and shocking.”

    Consider the fact that you are here asking for “evidence,” yet there is no evidence that you ever bothered to read the 14 essays that are linked to in the original blog entry above. How shall we interpret this glaring fact?

    1. You did not bother to read the 14 essays. The unwillingness to read the essays is evidence of a closed-mind, as a closed-minded person would not think it worth their time to read something that has been firmly rejected in their mind.

    2. You did read the 14 essays, but cannot come up with the single counterargument. In which case, you failed to acknowledge that you read the essays and are unable to shoot down the arguments. This too would indicate a closed-mind, as if your were unwilling to acknowledge that your opponent has made some good points.

    To this, we can add your most recent comment. I wrote the word “design” and your mind heard “God.” This form of conditioning indicates a superficial approach that would be expected to exist among the closed-minded.

    As I said, Nelson linked me here claiming I would find evidence for front loading. If he was mistaken, no problem, I’ll stop bothering you.

    You’re not bothering me. You’re evading a simple and important point – It depends if your skepticism is rooted in an open- and fair-minded approach that is sensitive to clues or if it is rooted in a closed-minded approach that demands something extraordinary and shocking. Are you willing to acknowledge that you adopt a closed-minded approach that demands something extraordinary and shocking?

  15. Much of a reality is not amenable to scientific study. If you disagree, perhaps you can explain why we don’t simply replace courtrooms and juries with scientists and labs.

    Discussion of the shortcomings of the US legal system would be, perhaps an interesting digression. Yes I disagree. All reality is amenable to scientific scrutiny. It is simply a matter of definition, anything that is unobservable or undetectable (however indirectly, images obtained from bubble chambers etc. are included in my reality) is not real for scientific purposes. What would be an example of a real thing that is not amenable to scientific scrutiny?

    And yes, you have evaded yet another question.

    (presumably this one?)

    Say, for the sake of argument, that life was indeed designed and thus evolution was front-loaded. Is there any reason to think science could discover this possible reality?

    Of course science can look for evidence of front loading (if you mean genetic sequences in genomes inserted for later use). The design question needs qualification. I don’t have a definition for “design” that conveys meaning in “life was designed”. I would have to have some idea of the type of designer we are considering, human, alien, other?

    It’s about evidence, Alan. As I noted, “I see no evidence that your skepticism is rooted in an open- and fair-minded approach that is sensitive to clues.” You have failed to provide any evidence to indicate I am wrong. Do you expect me to embrace opinions without evidence, Alan?

    I don’t expect you to embrace my opinions without evidence, any more than you should expect others to embrace yours. It would seem simplest to proceed on the basis that I will try and contain my scepticism and, as you hold all the cards whether to continue or cut off dialogue, you can accept that for the moment or not as you please.

    …yet there is no evidence that you ever bothered to read the 14 essays…

    You could always ask a couple of questions to check my comprehension.

    I wrote the word “design” and your mind heard “God.”

    He’s the only candidate for “Intelligent Designer” that I am aware of. Who else is proposed for the rôle?

    Am I to take it that there is scientific evidence of front loading in each of those 14 essays? “How to Guide the Blind Watchmaker” is top of the list. It goes into some detail about symbiogenesis (as first proposed by Lyn Marguys) and how mitochondria started out as free living prokaryotes. You pick up on a researcher’s phrase “…were available as a preadaptation…” and suggest that implies front loading. Is that the evidence?

  16. Excuse typos, with no preview it’s hard to spot them. s/b Lynn Margulis

  17. 8 comments from Alan and not a single attempt at a response to any of the essays. Can’t say I’m surprised.

  18. Hi Alan,
    I have no plans on cutting off any dialog. But I do think it best that we slow it down and take one thing at a time.

    You claimed, “I do not think there is any reality that is not amenable to scientific study.”

    So I replied, “Much of a reality is not amenable to scientific study. If you disagree, perhaps you can explain why we don’t simply replace courtrooms and juries with scientists and labs.

    You now reply:

    Discussion of the shortcomings of the US legal system would be, perhaps an interesting digression.

    This is evasion. You attempt to spin my point as if it is about “the shortcomings of the US legal system” and then, what’s worse, label it as a digression. No, I did not want to discuss the shortcomings of the US legal system nor is my point a digression.

    So let’s focus with some questions.

    1. Why did you try to spin things as if I was talking about “the shortcomings of the US legal system?”

    2. Why did you try to imply that I was raising a digression?

    3. Does the legal system deal with reality?

    4. Can you point to any country where the courtroom, judge, and jury have been replaced by scientists and labs?

  19. But I do think it best that we slow it down and take one thing at a time.

    Fine, but why don’t we make that one thing evidence for front loading. I am here because Nelson Alonzo claimed I could find it here.

  20. Mike, I’m disappointed though not surprised.

  21. Because I don’t know what you mean/want with your request for “evidence.” So please demonstrate your continued interest in dialog by answering my questions. Thank you.

  22. Nelson said I’d find it here.

    Answers:

    1. I’m not “spinning” anything. I don’t have a very high opinion of the US legal system. Maybe a panel of scientists would do a better job of establishing guilt or innocence.

    2. I think it was a digression. Maybe I’m missing a point you didn’t yet make. Is there an analogy for front loading to be found in considering the legal system?

    3. Yes.

    4. No.

  23. Q: Why did you try to spin things as if I was talking about “the shortcomings of the US legal system?”
    A: I’m not “spinning” anything. I don’t have a very high opinion of the US legal system. Maybe a panel of scientists would do a better job of establishing guilt or innocence.

    Since I did not mention anything about “the shortcomings of the US legal system,” and if you are not spinning, you should not have brought this digression up.

    Q: Why did you try to imply that I was raising a digression?
    A: I think it was a digression. Maybe I’m missing a point you didn’t yet make. Is there an analogy for front loading to be found in considering the legal system?

    The only digression was your attempt to make the issue about “the shortcomings of the US legal system?” How could my claim be a digression when it was a direct response to a truth claim you made?

    You claimed: “All reality is amenable to scientific scrutiny.”

    I replied: “Much of a reality is not amenable to scientific study. If you disagree, perhaps you can explain why we don’t simply replace courtrooms and juries with scientists and labs.”

    That’s not a digression. That’s a challenge to your core position that colors your perception.

    Q: Does the legal system deal with reality?
    A: Yes

    Q: Can you point to any country where the courtroom, judge, and jury have been replaced by scientists and labs?
    A: No

    Very good. So now it is time for you to go back and actually address my response:
    perhaps you can explain why we don’t simply replace courtrooms and juries with scientists and labs.

    BTW, you said that you are not a fan of pre-moderation. Sorry to inform you that I have set the blog so I have to approve all comments for the time being. Now, don’t get nervous or upset, as I will let your comments through when I check in. But since I can’t babysit the blog, it’s the only way I can ensure that our discussion is not interrupted or side-tracked by someone else.

  24. perhaps you can explain why we don’t simply replace courtrooms and juries with scientists and labs.

    Courts and juries are as they are mainly for reasons of history and inertia. It is simpler and less risky to leave things as they are rather than change them. Forensic evidence, especially would be better dealt with “inquisitorially”, that is evaluated by experts beforehand, so that issues of a technical nature are settled before any hearing,. So whilst I accept that juries and courts will gently evolve to maintain an appearance of effectiveness, there is not the political will to replace them with something better.
    I could develop this at length, but I doubt you are at all interested in my worthless opinions on crime and the effectiveness of the legal and judicial systems.
    As I keep saying, Nelson Alonzo said I would find scientific evidence for front loading here. Excuse my scepticism, but so far I am not encouraged.
    Re moderation. Fair enough, I’ll accept what you say though I think your fear of being inundated by trolls is unfounded.

  25. Hi Alan,

    Nelson directed me here to find scientific evidence for front-loading….. Guts seemed quite convinced there was evidence of ID (or at least front loading) to be found here….. As I said, Nelson linked me here claiming I would find evidence for front loading….. I am here because Nelson Alonzo claimed I could find it here…. Nelson said I’d find it here…. As I keep saying, Nelson Alonzo said I would find scientific evidence for front loading here.

    There is no need to repeat yourself obsessively, Alan. While it may be hard for you to believe, I was smart enough to get it the first time you mentioned this. Your constant repetition makes it sound like you implying I am too stupid to figure this out. Or perhaps you are Gut’s submissive, faithfully carrying out his orders. The fact remains that Guts did not force you to come here and is not forcing you to stay here. Please take responsibility for your own actions.

    Excuse my scepticism, but so far I am not encouraged.

    Irrelevant. Your favorite words are ‘scientific’ and ‘evidence’ (you’ve used them each eleven times in the few comments you have posted). Let’s not make the mistake in thinking that all brains are basically alike and assign the same meaning to words like “evidence” and “scientific.” So let’s get to the meaty stuff.

    Courts and juries are as they are mainly for reasons of history and inertia. It is simpler and less risky to leave things as they are rather than change them. Forensic evidence, especially would be better dealt with “inquisitorially”, that is evaluated by experts beforehand, so that issues of a technical nature are settled before any hearing,. So whilst I accept that juries and courts will gently evolve to maintain an appearance of effectiveness, there is not the political will to replace them with something better.
    I could develop this at length, but I doubt you are at all interested in my worthless opinions on crime and the effectiveness of the legal and judicial systems.

    So the only reason why scientists and labs have not replaced courtrooms, judges, and juries is because of “history and inertia” and a lack of “political will” anyplace on this planet, right? Please answer.

    What I am interested in is your vision of how this scientific justice system would work. Are you just imagining a “panel of experts,” sort of like making sure scientists are the jury members or judges? Or are you talking about actually doing science? Please answer this question.

    Finally, you acknowledged (the third question) that courtrooms deal with reality. Doesn’t this mean we can deal with reality, however flawed, outside of the scientific community? Please answer this question.

  26. Mike.

    Yes, yes and yes.

  27. Hi Alan,

    In regards to the third question, it is good that we agree on the obvious – that the legal system deals with reality and thus we can deal with reality without having to do science. So one wonders why it is so important to you that the evidence must be “scientific.”
    It would be irrational, for example, to dismiss all courtroom verdicts as fantasy simply because they are not scientific.

    On the other hand, you seem to conflate reality with science: “And I do think that science is defined by reality and vice versa. I do not think there is any reality that is not amenable to scientific study.”

    So we are left wondering why it is that the reality addressed by courtrooms is not instead a matter of scientific study, as we once again agree on the obvious – no where on this planet can we find a place where the scientific process has replaced the legal system.

    I think the explanation is rather straightforward – the scientific process cannot replace the legal system because the scientific process cannot settle the disputing reality claims that take place in the courtrooms. Yes, in many cases, scientific analysis can and does play a role in the courtroom, as one consideration in the overall argument, but that is not the same as replacing the courtroom process.

    You explain it by invoking sociological factors – “history and inertia” and a lack of “political will.” I think this is nonsense given there is no evidence these are the obstacles; along with the way this explanation implies scientists are lazy and/or cowardly. If scientists could conduct studies that resolved courtroom disputes about reality, they would have done so long ago to develop a track record sufficient to generate the “political will” for such a transformation. In fact, the system is already set up to accommodate for this. Many scientists work at universities and, as such, could use scientific research to substitute for panel deliberations in student misconduct or sexual harassment disputes within the university. The reason scientists don’t bother is that they know scientific research cannot, by its nature, substitute for such panels. Some reality claims simply cannot be resolved with scientific scrutiny.

    There is yet another problem with your position. According to you, the reason science has not replaced the legal system is because of sociological and political reasons. But that means that the topics addressed by science are the function of sociological and political decisions. So follow me here. You say “science is defined by reality and vice versa,” yet your position here tells us that science is defined by history, inertia, and political will (since science is what science addresses). If science = reality, this would mean that reality is defined by history, inertia, and political will.

    Lastly, as for the second question, ‘yes’ doesn’t answer it. It was a choice: Are you just imagining a “panel of experts,” sort of like making sure scientists are the jury members or judges? Or are you talking about actually doing science?

  28. Are you just imagining a “panel of experts,” sort of like making sure scientists are the jury members or judges? Or are you talking about actually doing science?

    Both.

    May I ask a question?

    Is there a possibility that we can discuss your ideas on front loading at some stage?

    I’m not insisting on a yes or no answer but some indication would be appreciated.

  29. If you are interested here is a thread at ARN where I try to expand on the concept of reality and imagination with regard to what is amenable to scientific study. It’s possible it may answer questions you still have on what my position is.

  30. Oh and…

    I recently discovered there is a doctrine called scientific realism that seems to fit me as a category.

    But this is not about me…

  31. Mike, presumably you have my email. Perhaps you could give me a heads up when you post a comment intended for me.

    Cheers
    Alan

  32. Hi Alan,
    Let’s move on to the next portion of your reply:

    Yes I disagree. All reality is amenable to scientific scrutiny. It is simply a matter of definition, anything that is unobservable or undetectable (however indirectly, images obtained from bubble chambers etc. are included in my reality) is not real for scientific purposes. What would be an example of a real thing that is not amenable to scientific scrutiny?

    I’m not sure why you ask me this question when a) I provided such an example and b) you deleted and ignored it. Let’s try again:

    Or look at it this way. You came to this blog making a claim about reality: “Point of information, an ISP check should clarify that the first post is not from me.”

    So I checked the IPs and they were indeed different, leading me to confirm your claim about reality. Are you saying I used science to confirm your claim about reality and thus made a scientific discovery?

    Then again, it is possible for people to post using more than one IP. So it is possible that you were lying and did indeed post the first comment from ‘Alan Fox.’ How would science determine that you were not lying?

  33. I don’t expect you to embrace my opinions without evidence, any more than you should expect others to embrace yours. It would seem simplest to proceed on the basis that I will try and contain my scepticism and, as you hold all the cards whether to continue or cut off dialogue, you can accept that for the moment or not as you please.

    I don’t care if you contain your skepticism or not. You originally asked , “Do you have something that might dent my scepticism?” I then informed you that it depends if your skepticism is rooted in an open- and fair-minded approach that is sensitive to clues or if it is rooted in a closed-minded approach that demands something extraordinary and shocking. Apparently, this point has not sunk in for you.

    There is no evidence that your skepticism is rooted in an open- and fair-minded approach that is sensitive to clues and there is growing evidence that it is rooted in a closed-minded approach. Thus, your original question should be re-worded in a way that more accurately reflects reality. Instead of ‘Do you have something that might dent my scepticism?’ it should read “Do you have something that might dent my disconfirmation bias?’

    And that’s a silly question.

    Now, when I drew attention to your lack of interest in the arguments/evidence linked in the original blog entry , you replied:

    You could always ask a couple of questions to check my comprehension.

    Now, you contradict yourself. You just told me, “I don’t expect you to embrace my opinions without evidence.” To ask a question about your comprehension I would have to hold the opinion that you read the essays. Since there was no evidence that you ever bothered to read the essays, why would you ever expect me to hold that opinion and ask such questions of you? You seem to be willing to abandon your evidence/reality schtick when it suits you.

    Of course, now that I have put the light on your closed-minded disinterest in the essays linked in the blog entry, suddenly you want to posture as if you had read them. So let’s raise another example of a real thing that is not amenable to scientific scrutiny. Before I noted your disinterest in the essays, you either read the essays or you did not. Either one, but not both, is part of reality. How would I use science to determine whether you read the essays or not before this comment?

  34. You came to this blog making a claim about reality…

    I came to this website because Nelson Alonzo linked to it at Telic Thoughts. Visit the site and click my name. It links here. Childish of Nelson, but there you are.

    I have to ration my time here, Mike, so I would rather you live with my scepticism and I’ll live with your condescension.

  35. Hi Alan,

    It’s easy to live with your skepticism given its impotence (none of the points of those 14 essays have been debunked). But you should pause to consider what makes it so ineffectual. Consider the track record you have already established in the short time you have been posting here:

    – you have a tendency to evade my questions
    – you are incapable of acknowledging when I make a good point
    – you ignore arguments that are inconvenient for your position
    – you are reluctant to read my arguments and make a good faith attempt to understand them
    – you’d rather pass judgment than seek mutual understanding

    This is not mere skepticism, Alan. This is classic closed-minded, disconfirmation bias on your part. And if disconfirmation bias is in play when it comes to these issues, it clearly will be in full closed-minded force if it came to any “discussion” about the “evidence” for front-loading. It would be irrational to expect to otherwise.

    I’m sorry you feel my exploration of reality is condescension.

  36. Alan,

    Since you are unable to answer the questions and arguments I have raised, I understand your newly discovered need to “ration” your time. But don’t lose sight of the fact that you just made another reality claim – “I have to ration my time here, Mike.”

    According to you, “All reality is amenable to scientific scrutiny.” So how would I use science to determine you are telling the truth about this need to ration your time?

    You have now made three reality claims without telling us how science would scrutinize them.

  37. So going back to your essay entitled “How to Guide the Blind Watchmaker”

    You quote Perry A.J et al

    These distinct ancestral TPR proteins independently gave rise to the Tom20 in plants and the Tom20 in animals and fungi.

    hypothesizing that plant Tom20 and animal/fungi Tom20 are not homolgous. You then write:

    In this case, natural selection did not stumble upon some solution, any solution, that just happened to work. No, no. It hit the same target – twice. And it did so roughly about the same time: after plants and animals/fungi split apart, but before animals and fungi split apart, and before green algae and plants split apart.

    I assume you are suggesting that such a result is so unlikely as to be impossible by evolutionary processes alone. But this is just an argument aginst the current theory, unless you are proposing an alternative mechanism.

  38. I assume you are suggesting that such a result is so unlikely as to be impossible by evolutionary processes alone. But this is just an argument aginst the current theory, unless you are proposing an alternative mechanism.

    You assume wrong, Alan. My position has never revolved around any attempt to show that something is impossible by evolutionary processes alone. So why would you assume that about my essay?

    These types of errors on your part are likely to replay again and again and again. Why? Because you won’t come to terms with your own closed-mindedness. Because you are closed minded, you skimmed through that essay with disconfirmation bias. And science has helped us to understand how that works:

    When faced with evidence contrary to their beliefs, people try to undermine the evidence. That is, there is a bias to disconfirm arguments incompatible with one’s position. This idea can be developed into a disconfirmation model by making the following assumptions.

    1. When one is presented an argument to evaluate, there will be some automatic activation in memory of material relevant to the argument. Some of the accessed material will include one’s prior beliefs about the issue.
    [….]
    3. Possible targets of the memory search include stored beliefs and arguments that offer direct evidence against the premises and conclusion of the presented argument.

    Clearly, your brain’s attempt to force my arguments into the “it’s impossible for evolutionary mechanisms” was due to the dynamics laid out in 1. Or put more simply, when you are closed-minded, you’ll need to rely on stereotypes.

    The need to see the essay in this light is then coupled to the fact that your mind thinks it has a pre-ready refutation to play (number 3), which explains why you offered a counter-argument to the figments of your assumptions (“But this is just an argument aginst the current theory, unless you are proposing an alternative mechanism.”)

  39. My position has never revolved around any attempt to show that something is impossible by evolutionary processes alone.

    I would hope not, as I would really be wasting my time 😉
    Are you working towards a hypothesis of front loading, where you are able to make a prediction that could be verified by observation or experiment?

    By the way is there something that describes what your idea of front loading actually is?

  40. If this means going over old ground, perhaps you could suggest some reading. The thread here on your blog did not really end up throwing much light on what front loading might be as a mechanism or whether it supplements or replaces RM + NS (It seems to have ended rather abruptly). John Davison, who claims to have the only real mechanism for front loading, has his evolutionary manifesto and his prescribed evolutionary hypothesis. Perhaps you have an equally useful summary of the salient features of front loading?

  41. test

  42. I would hope not, as I would really be wasting my time

    Oh, but you assumed just that. Your hopes are not relevant. Your actions are. So please explain why you did assume that.

  43. My position has never revolved around any attempt to show that something is impossible by evolutionary processes alone.

    So what is front loading according to Mike Gene? Does it replace or supplement RM + NS? Am I right in saying that you don’t claim intelligent design (hence, presumably, front loading) is yet a viable scientific theory? If this is so, and front loading is not currently a viable scientific theory, can there nonetheless be scientific evidence for it?

  44. LOL, Alan. For a man who needs to ration his time so much, you sure have been busy pounding on the door to get my attention while I was away. Look, I know it is difficult to ignore me, but try to remember that I have this blog set so I must approve comments. And during the work week, I can’t get to that until the real world is done for the day.

    Are you working towards a hypothesis of front loading, where you are able to make a prediction that could be verified by observation or experiment?

    Sure. The hypothesis of front-loading has already allowed me to expect several things about biotic reality that turned out to be true.

    By the way is there something that describes what your idea of front loading actually is?

    Yep. The logic is outlined in chapter 7 of TDM. Of course, it is all a work in progress and this blog builds on the various themes that are outlined in the book. Also, if you check out the front page of this blog, on the right side is a section called ‘Tags.’ You’ll notice the tag in largest font is front-loading. Click on it and you can survey many of the essays that are relevant to front-loading.

    So what is front loading according to Mike Gene?

    Here is a recent attempt to explain the concept.

    These may also be of help:

    https://designmatrix.wordpress.com/2009/01/17/misunderstandings-about-front-loading/
    https://designmatrix.wordpress.com/2009/01/23/misunderstandings-about-front-loading-2/
    https://designmatrix.wordpress.com/2009/02/10/misunderstandings-about-front-loading-3/

    Does it replace or supplement RM + NS?

    Front-loading is about whether or not RM + NS can be guided. It may be a subtle distinction that you will not be able to grasp. I say this because you supposedly read one of my essays where I explore possible ways to guide RM + NS and immediately assumed I was arguing evolution was impossible. Go figure.

    It would also help if you tried to understand the basic metaphor that underlies my whole approach.

    Am I right in saying that you don’t claim intelligent design (hence, presumably, front loading) is yet a viable scientific theory?

    Of course. In fact, I do not think science can ever determine whether or not front-loading is true.

    If this is so, and front loading is not currently a viable scientific theory, can there nonetheless be scientific evidence for it?

    It depends on what you mean by “scientific evidence,” as I have discovered from my years of interacting with many skeptics that it means different things to different people.

  45. Thanks Mike. That should keep me quiet for a while. Though I do wonder why you couldn’t have just posted that as your first response to me. I’ll get back to when I’ve had a chance to read through the stuff.

    I’ll not take the bait about “pounding on the door” and you can believe me or not that I have to take opportunities to comment as they arise and I quite appreciate that you like most people have time management problems. Maybe you should set up your last response as a FAQ.

  46. Though I do wonder why you couldn’t have just posted that as your first response to me.

    Hmmm. Compare

    Do you have something that might dent my scepticism?

    with

    So what is front loading according to Mike Gene?

  47. you can believe me or not that I have to take opportunities to comment as they arise

    But why should I have to do this? According to you, “All reality is amenable to scientific scrutiny.” Why should I have to believe when we have science?

    Clearly, this notion that all reality is amenable to scientific scrutiny is false.

  48. Me:

    …you can believe me or not that I have to take opportunities to comment as they arise…

    Mike Gene:

    But why should I have to do this? According to you, “All reality is amenable to scientific scrutiny.” Why should I have to believe when we have science?
    Clearly, this notion that all reality is amenable to scientific scrutiny is false.

    I can’t follow your logic here, Mike. My statement was meant to convey “I don’t care whether you believe anything I say, but in case you do, my time available for commenting here is variable and limited” but more politely! So you don’t have to. You have free will, you can choose whether to accept all, some or none of my assertions. How does this falsify the working assumption that “real” and “scientifically detectable” are synonymous? Nothing you have written in these comments so far explains how you justify your apparent belief that reality in courtrooms differs from reality in general.

  49. Still reading your stuff. Have house guests for another week, so availability of computer time is very sporadic.

  50. Hi Alan,

    Reality is reality. But not all reality is amenable to scientific scrutiny. That’s we have courtrooms. That’s why I must rely on faith when deciding (or not) to believe your reality claims about yourself in this thread. I’m not sure why you would think otherwise.

  51. Still reading your stuff. My very out-of date undergraduate biochemistry is proving inadequate to the task. I recall a seminar early in my first year discussing protein synthesis and wondering how a genome incorporating a genetic code that only started, produced sequences of amino acids and stopped could result in an adult human developing from a single cell. My thought “there must be more to it” seems to have been reasonable in hindsight. How the knowledge base of molecular biology has expanded since 1970!

    Back to evidence for front loading. I have read through your articles on the signal recognition particle and its role in secretion, where you make references to front loading. I must be missing something. The primary literature on SRPs seems pretty cutting edge and there is plenty of “we don’t know” that can be inferred, but I am still not seeing “the design inference”. You, I predict, are now going to tell me I am not open minded enough to which I would respond that “we don’t know” is a more open-minded approach than” we don’t know which is evidence for design”.

  52. Reality is reality. But not all reality is amenable to scientific scrutiny.

    We have to agree to disagree, then. Science is defined by its inability to address unreality, and anything that is real is available for scrutiny.

    That’s we have courtrooms.

    Disagree. DNA evidence is a highly effective tool in the fight against crime. Video surveillance and other technical innovations improve detection and conviction. In former times, jury decisions have, where studies have been done, been little better than coin tossing at correctly establishing guilt or innocence.

    That’s why I must rely on faith when deciding (or not) to believe your reality claims about yourself in this thread. I’m not sure why you would think otherwise.

    If the issue was at all important (such as my being a murder suspect and my alibi depended on showing it was me posting a comment from a particular terminal at a particular time) then forensic analysis could settle the matter.

  53. Hi Alan,

    Back to evidence for front loading. I have read through your articles on the signal recognition particle and its role in secretion, where you make references to front loading. I must be missing something. The primary literature on SRPs seems pretty cutting edge and there is plenty of “we don’t know” that can be inferred, but I am still not seeing “the design inference”.

    We can discuss this, but let’s wait until the series is done. I figure I should be able to get 3-4 more to finish up the story. Besides, I have always had this blog set up so that the comments section will automatically close after 60 days (an effective way to cut down on the spam). Since this particular entry will close up on Nov 1, we might want to move that discussion to the last entry in the series. So you’ll be able to tell when I am done, look for the bunny in sunglasses.

    You, I predict, are now going to tell me I am not open minded enough to which I would respond that “we don’t know” is a more open-minded approach than” we don’t know which is evidence for design”.

    No, I will not make any judgment about you being closed or open-minded as a consequence of your reaction to arguments regarding front-loading. I have never done this and don’t plan on starting now. What I did do was to make such a judgment independent of any FLE discussion, based on the pattern of behavior shown prior to any such discussion.

    I agree that “we don’t know” is a more open-minded approach than “we don’t know which is evidence for design”. The latter position presupposes the evidence exists but says we don’t know what it is. My own position is to recognize that none of us will ever truly understand what happened so long ago. None of us know. But I am surrounded by people who either insist there is no (!) evidence for design or that the evidence for design is overwhelming. They think they know. I don’t empathize or understand their sense of certainty of these issues. All I can do is explore the vast unexplored middle ground between these two extremes, while following up on hunches and suspicions. After all, the down-side to “we don’t know” is that it doesn’t satisfy curiosity.

  54. Hi Alan,

    We have to agree to disagree, then. Science is defined by its inability to address unreality, and anything that is real is available for scrutiny.

    But the problem is that I easily found three examples (in this thread alone) of reality claims that cannot be resolved by science.

    Disagree. DNA evidence is a highly effective tool in the fight against crime. Video surveillance and other technical innovations improve detection and conviction. In former times, jury decisions have, where studies have been done, been little better than coin tossing at correctly establishing guilt or innocence.

    I never denied that science can often play a role in the courtroom. I just can’t replace it. I explained this above: “I think the explanation is rather straightforward – the scientific process cannot replace the legal system because the scientific process cannot settle the disputing reality claims that take place in the courtrooms. Yes, in many cases, scientific analysis can and does play a role in the courtroom, as one consideration in the overall argument, but that is not the same as replacing the courtroom process.”

    If the issue was at all important (such as my being a murder suspect and my alibi depended on showing it was me posting a comment from a particular terminal at a particular time) then forensic analysis could settle the matter.

    This is an interesting claim on many levels.

    First, if true, it means that science only studies what the social group decides is “important.” This would mean that science gives us a selective perspective of reality that can be very misleading, simply as a function of topics that are ignored or deemed “unworthy.”

    Second, I doubt this very much. Such forensic analysis would not be able to tell if it was you posting, as someone else could have had access (with or without your knowledge) to your cyber life.

    Third, would such a forensic analysis truly be science? That’s why I twice asked the following up above:

    Or look at it this way. You came to this blog making a claim about reality: “Point of information, an ISP check should clarify that the first post is not from me.”

    So I checked the IPs and they were indeed different, leading me to confirm your claim about reality. Are you saying I used science to confirm your claim about reality and thus made a scientific discovery?

  55. We can discuss this, but let’s wait until the series is done. I figure I should be able to get 3-4 more to finish up the story. Besides, I have always had this blog set up so that the comments section will automatically close after 60 days (an effective way to cut down on the spam). Since this particular entry will close up on Nov 1, we might want to move that discussion to the last entry in the series. So you’ll be able to tell when I am done, look for the bunny in sunglasses.

    Fair enough. I am somewhat reassured about your moderation policy though I found Akismet is almost 100% effective against spammers.

    If I were in a mood to be snarky I could point out Nelson’s claim was that scientific evidence for front loading was already to be found here but no worries!

  56. I agree that “we don’t know” is a more open-minded approach than “we don’t know which is evidence for design”. The latter position presupposes the evidence exists but says we don’t know what it is. My own position is to recognize that none of us will ever truly understand what happened so long ago. None of us know. But I am surrounded by people who either insist there is no (!) evidence for design or that the evidence for design is overwhelming. They think they know. I don’t empathize or understand their sense of certainty of these issues. All I can do is explore the vast unexplored middle ground between these two extremes, while following up on hunches and suspicions.

    Well said, sir! Nothing to argue with here.

    After all, the down-side to “we don’t know” is that it doesn’t satisfy curiosity.

    But surely, one can attempt to find out and that may satisfy our curiosity for the moment.

  57. This is an interesting claim on many levels.

    First, if true, it means that science only studies what the social group decides is “important.” This would mean that science gives us a selective perspective of reality that can be very misleading, simply as a function of topics that are ignored or deemed “unworthy.”

    The practical issue is funding, so, in a sense, social groups can constrain scientific research. But the theoretical limit is reality.

    Second, I doubt this very much. Such forensic analysis would not be able to tell if it was you posting, as someone else could have had access (with or without your knowledge) to your cyber life.

    I was not just thinking of the ISP record. There is also analysis of language and spelling patterns, physical evidence left on the keyboard or elsewhere in my office, evidence of my presence elsewhere at relevant times. Obviously the whole panoply of available techniques would only be brought to bear in a situation that merited it.

    Third, would such a forensic analysis truly be science?

    I would hope it would be scientific, especially if my defence against murder depended on it!

    That’s why I twice asked the following up above:

    Or look at it this way. You came to this blog making a claim about reality: “Point of information, an ISP check should clarify that the first post is not from me.”

    So I checked the IPs and they were indeed different, leading me to confirm your claim about reality. Are you saying I used science to confirm your claim about reality and thus made a scientific discovery?

    You used the scientific method. You checked available evidence and used it to confirm my assertion.

  58. HTML tags error.

    “You used the scientific method. You checked available evidence and used it to confirm my assertion.”

    is my response. I’m sure a preview facility is available in wordpress.

  59. Fair enough. I am somewhat reassured about your moderation policy though I found Akismet is almost 100% effective against spammers.

    Akismet is too good – it sometimes captures legitimate comments and throws them into the spam pile. And I don’t enjoy manually looking through dozens of spam postings to be sure there is nothing legitimate in them before I dump them all. My solution has turned out to be quite effective, as the open threads (which act as spam magnets) are kept minimal and the spam pile is easy to look through in a periodic manner. Besides, a survey of most blogs will show very little to no discussion in blog entries older than 60 days (unless some people are caught up in an ego war).

    If I were in a mood to be snarky I could point out Nelson’s claim was that scientific evidence for front loading was already to be found here but no worries!

    And I could return the snark by noting that after three weeks posting here, there is evidence that you superficially skimmed only one of the fourteen essays Guts had in mind. I could also note that you have not refuted one point in any of those fourteen essays.

  60. The practical issue is funding, so, in a sense, social groups can constrain scientific research. But the theoretical limit is reality.

    In a practical sense, social groups DO constrain scientific research. Funding is just one expression of what the group deems “important.”

    As for the theoretical limit, just because what science studies is reality does not mean science can study all reality. Apart from the examples I have already cited, consider the simple historical fact that the reach of science is a function of its ability to measure and observe. For example, prior to the telescope or microscope, huge spans of reality were beyond the reach of science.

    I was not just thinking of the ISP record. There is also analysis of language and spelling patterns, physical evidence left on the keyboard or elsewhere in my office, evidence of my presence elsewhere at relevant times. Obviously the whole panoply of available techniques would only be brought to bear in a situation that merited it.

    I’m not sure you’ll get much in terms of language analysis and spelling patterns with “I see no evidence for front-loading.” In fact, you yourself replied, “On the other hand, I don’t see any evidence for front loading either.” As for the other stuff, I fail to see how any of it would resolve this issue.

    Nevertheless, if we get to the bigger point you are making, the only thing this forensic analysis provides is circumstantial evidence where, in the end, subjective judgment calls will be needed. In the current courtroom system, forensic data plays a huge role in many cases. But that is not the same as being able to replace the courtroom system.

    Consider, for example, that while the whole panoply of available techniques could be brought to bear in a situation, it still remains the fact that the number of unsolved crimes vastly outnumbers the number of solved crimes. And when we do solve a crime, it still remains a subjective judgment call in the end, unless the suspect confesses to the crime.

    I would hope it would be scientific, especially if my defence against murder depended on it!

    Okay, here is where we have a element of miscommunication. I inquired about a verb – “doing science,” and you replied about an adjective – scientific. Just because a belief includes facts discovered by science does not mean the belief itself is scientific. It depends on how we define “science” and “scientific” and I have found that the definitions of those popular words depend on the person defining them.

    You used the scientific method. You checked available evidence and used it to confirm my assertion.

    A good example of what I am talking about. You seem to have a watered-down perception of science, while I have a much more rigorous perception of science. Just because I investigated a small part of reality and discovered a fact (the IPs were not the same) does NOT mean I was doing science nor does it mean I can cite this as a scientific discovery. But if the water-down perception says otherwise, we can apply it across the board. We can explore why it is that finding different IPs to support a personal reality claim is science, but why some of those essays are not.

  61. You used the scientific method. You checked available evidence and used it to confirm my assertion.

    Look at it this way. Many of the essays posted on this blog used the same “scientific method”- I checked available evidence and used it to strengthen suspicions. I don’t think of this as science (and for this reason, many of the ID people don’t like me). But if I am indeed doing science to when I do something as mundane as checking to see if IPs are different, how is it that I am not doing science when I use the hypothesis of front-loading to check if ribosomal proteins have multiple functions?

  62. But if I am indeed doing science to when I do something as mundane as checking to see if IPs are different, how is it that I am not doing science when I use the hypothesis of front-loading to check if ribosomal proteins have multiple functions?

    You are doing science whenever you are dealing with reality! If there is a real hypothesis of front loading according to Mike Gene that is capable of being falsified by testing its predictions, then that’s science!

    However, I am still not at all clear what your hypothesis is and what it predicts.

    I am now reading the primary papers and I thought it might be interesting to email Professors Trevor Lithgow and Paul Gooley to see what they think of your interpretation of their work. I’ll keep you posted on a newer thread.

  63. Hi Alan,

    You are doing science whenever you are dealing with reality!

    Wrong. Whenever I blow my nose, or take the kids swimming, or run to the store to buy milk, I am dealing with reality, but NOT doing science.

    If there is a real hypothesis of front loading according to Mike Gene that is capable of being falsified by testing its predictions, then that’s science!

    Testing a hypothesis is a necessary condition of science, but not sufficient to call something science. We all test all kinds of hypotheses in our daily life. But that does not mean we are all scientists making scientific discoveries everyday. Like I suspected, you have a watered-down perception of science. It is absurd that you would think my simple IP check was a scientific discovery.

    However, I am still not at all clear what your hypothesis is and what it predicts.

    One formulation of the hypothesis is FLE is: the original cells were endowed with a set of preadaptations that would channel and guide subsequent evolution. More specifically, they contained features and architecture that served as preadaptations to facilitate the evolution of multicellular, metazoan existence.
    The hypothesis of front-loading evolution would thus predict that significant transitions in evolution (the origin of metazoan) would depend on preadaptation.

    I am now reading the primary papers and I thought it might be interesting to email Professors Trevor Lithgow and Paul Gooley to see what they think of your interpretation of their work. I’ll keep you posted on a newer thread.

    Sounds good to me.

  64. Me:

    You are doing science whenever you are dealing with reality!

    Mike Gene:

    Wrong. Whenever I blow my nose, or take the kids swimming, or run to the store to buy milk, I am dealing with reality, but NOT doing science.

    If you disagree with the statement “You are not doing science whenever you are not dealing with reality” then there is an issue. If not, that’s fine. It is more usual for ID proponents to wish to shoe horn the imaginary into science. I have no problem if you want to stay closer within the absolute limits of scientific enquiry.

    Me:

    If there is a real hypothesis of front loading according to Mike Gene that is capable of being falsified by testing its predictions, then that’s science!

    Mike Gene:

    Testing a hypothesis is a necessary condition of science, but not sufficient to call something science. We all test all kinds of hypotheses in our daily life. But that does not mean we are all scientists making scientific discoveries everyday. Like I suspected, you have a watered-down perception of science. It is absurd that you would think my simple IP check was a scientific discovery.

    You don’t know what I think. Plus I didn’t say it was a “scientific discovery” though you were verifying available evidence.

  65. If you disagree with the statement “You are not doing science whenever you are not dealing with reality” then there is an issue. If not, that’s fine.

    Why would I disagree with that statement? I fully understand that, for example, when I go immerse myself in a movie, I am not doing science. The issue is your false assertion:

    You are doing science whenever you are dealing with reality!

    Wrong. Whenever I blow my nose, or take the kids swimming, or run to the store to buy milk, I am dealing with reality, but NOT doing science.

    Why do you want to water-down the definition of science so much that you end up equating it with blowing your nose?

    It is more usual for ID proponents to wish to shoe horn the imaginary into science.

    Thar she blows! It was just a matter of time before you made it clear you have been relying on stereotypes.

    You don’t know what I think.

    You are putting your thoughts in writing and I am applying them. You think we “are doing science whenever you are dealing with reality!” Your words. Your position. You even added an exclamation point, as if your perception was supposed to be obvious or important.

    Plus I didn’t say it was a “scientific discovery” though you were verifying available evidence.

    I know. I asked you twice about this and you twice evaded the question. It’s entailed in the logic of your belief system, Alan. You believe we are doing science whenever we are dealing with reality. In doing an IP check, according to you, I was dealing with reality, thus doing science. In doing an IP check, I made a discovery. Since I made a discovery while, according to you, doing science, your belief system would categorize that as a scientific discovery.

    I understand you don’t want to say this, as it is ridiculous to categorize my IP check as a scientific discovery and you seem to recognize this. But since it follows from your position about science, your position about science is ridiculous. Do you recognize this yet?

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