Monday, May 09, 2016

Research for a book

I'm on sabbatical this term, working on a possible book whose working title is "What's in Your Genome?: 90% of your genome is junk."

Here's some of the most important books I've read (or re-read) in the past few months.


I've also read a lot of papers and scribbled notes on what's important and what's bullshit not. The most difficult part about keeping up with the scientific literature is organizing it in some meaningful way so you can quickly find it again if you need to—something I do just about every day.

Everyone has their own method. What works for me is to keep an electronic reference with key words and links to a file folder on a particular topic. (I use EndNote.) Here are the folders with all the papers I've been reading in the past few months.


I don't know how other authors behave but for me the most difficult thing about writing a book is organizing my thoughts and planning how to present them in the most effective manner. I tend to write too much on too many topics so the initial drafts usually have to be pared down considerably. Keeping that in mind, what are YOUR favorite topics?


258 comments :

  1. Your souper vs smoker series has been very enjoyable

    Thomas Robert Cech tends to see vestiges of the RNA world where others do not.

    Clearly, the Ribosome can be understood as a Ribozyme decorated with Protein.

    I would be very interested if any other examples could pass your skeptical muster.

    ReplyDelete
  2. A "Brief history of genomic research" section is a must. Remind people of genetic load, c-value paradox, central dogma, etc. Its seems that at least half of the arguments against junk DNA stems from misunderstanding - or not even knowing about - these concepts.

    ReplyDelete
    Replies
    1. Chapter 6, "Why Don't Mutations Kill Us?" is about genetic load.

      Chapter 8 is "The C-Value Paradox." It begins with a warning about eating fugu sashimi.

      There's a section on the Central Dogma in Chapter 4 ("What Is a Gene?).

      Delete
    2. "What is a gene?" That chapter I definitely will want to read!

      Delete
  3. Alternative title: most of your genome is junk - get over it!

    ReplyDelete
    Replies
    1. The tentative title of the last chapter is "Zen and the Art of Coping with a Poorly Designed Genome."

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

      Delete
    3. Function, not purpose. Don't anthropomorphise DNA, it doesn't like it.

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

      Delete
    5. If you don’t want me to anthropomorphize DNA, then don’t use a term that leaves me no choice but to do so.

      Do what ever you want. I don't care.

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

      Delete
  4. Somewhere near the beginning, the "players" - a list of the most common types of valuable stuff, and the most common types of junk, with approximate percentage ranges for each. Then either collocated with this initial list or in separate chapters, explanations of what each of the valuable things do, and how we know each of the types of "junk" are indeed junk.

    I think working this way - explaining the "right stuff" first, so people have a framework to use in evaluating all the incorrect claims - is best.

    ReplyDelete
    Replies
    1. Chapter 2 is "The Big Picture." It's an overview of all the things in the human genome with best guesses as to frequency (i.e. 1.25% protein-coding, 27% introns).

      There are separate chapters on genes, pseudogenees, and ORFans (Chapter 4); tranposons, viruses, and satellite DNA (Chapter 5); pervasive transcription and functional RNAs (Chapter 11); regulatory sequences (Chapter 12); and bulk DNA hypotheses, including chromatin structures (Chapter 13).

      Delete
  5. "...I'm on sabbatical this term..."

    I just hope it was a voluntary sabbatical...

    Here is an idea for the title of your book:

    "If more than 10% of human genome is not junk-I will become a creationist."

    This title has more punch and it is much more likely to attract attention of possible publishers even if your book is shit or turns out to be shit. I know something about it. I published one or two books.

    ReplyDelete
    Replies
    1. Do you even know what a sabbatical is, Eric?

      Are you saying that the Discovery Institute is predicting that as much as 89% of the human genome may be junk?

      Delete
    2. "Dude, he published one or two books."

      And according to Eric they were shit. He knows something about it.

      Delete
    3. I've been on sabbatical more than once. That's why I've asked Larry the specific question. It all depends on an institution or company you work for how they view or interpret "sabbatical".
      Some institutions grant you a paid sabbatical, and some say you can take a sabbatical and pay for your expenses but we ain't paying for it or we are not paying you when you are gone. (the sabbatical part it is that you are still employed with the company when you come back)

      As an example;

      Doctors in Ontario can take a sabbatical (for one reason or another) but if the institution that employs them doesn't pay them while they are gone or doesn't have a sponsor that pays their expenses and wages, they are on their own...

      Delete
    4. Eric, you didn't ask me a specific question.

      You know that I'm a university professor. All major universities have pretty much the same rules about sabbaticals. If you don't know what they are then look them up or ask. Otherwise you just look like an idiot.

      Delete
    5. I am still interested in seeing if Eric can clarify his statement implying that creationism is consistent with up to 90% of the genome being junk. That's quite different from many of the most prominent IDiots claim. I wonder if Eric has discussed that with them.

      Delete
    6. Creationism can be close to 100% of functionality. I personally think that no matter what the discoveries reveal, the vere few on the other side will always question it whether they have a legit reason for it or not.

      Unfortunately, today, one can't question anybody's feeling about anything. If a human feels he is a snake or a robot, you have to accept that....

      What difference does it make if Larry married himself to junk DNA'? Can you get him fired if he is wrong? Can you discipline him if he is wrong?

      I don't think so... and this is the saddest part of this society that can't function as it is, if no one can be accountable for their actions; this is a perfect example.

      Delete
    7. Eric,

      "Creationism can be close to 100% of functionality."

      Why would creationism predict close to 100% functionality? If the genome is not close to 100% functional, will you abandon creationism?

      "I personally think that no matter what the discoveries reveal, the vere few on the other side will always question it whether they have a legit reason for it or not."

      Much like you cling to claims of close to 100% functionality when there is so much scientific evidence against it.

      Delete
  6. Looking forward to anything you write!

    ReplyDelete
  7. I would like to see something on evolution of genome size. How much variation exists within and between species. How fast can genome size change? What causes that?
    I guess Michael Lynch already covered a lot of that in his book (and I can see it on your shelf), but some background on this will help explain how we ended up with so much non-functional DNA.

    ReplyDelete
    Replies
    1. I've crammed most of that into chapters on "Sequence Conservation" (Chapter 7) and the chapter on the C-Value Paradox (Chapter 8).

      It's really hard to organize some of this material since all the subjects are related to each other and you can't really discuss one without mentioning the others. For example, in discussing the evolution of genome size you have to know about modern evolutionary theory but in order to understand why neutral alleles and drift are important you have to understand that there's a problem in the first place (i.e. large complex genomes).

      In order to discuss the evolution of genome size you have to appreciate that most of it is junk. And you have to understand there's a difference between active, functional, transposons and defective versions that litter our genome. You also have to understand why deletions and insertions are important, which means a chapter on mutations (Chapter 6).

      There's no easy way to do this properly. This is one of the main reason why Intelligent Design Creationists (and the general public) have so much trouble understanding the science.

      Delete
    2. I think it is also very important to note that the correlation between ne and genome size is not a hard and fast rule. There are several exceptions to it. Fierst et al, "Reproductive Mode and the Evolution of Genome Size and Structure in Caenorhabditis Nematodes" provide a nice example. I believe Eugene Koonin also published a paper on this, but I cannot locate it right now.

      Delete
    3. @Wyatt Clark

      Yes, the relationship is a correlation not a hard and fast mathematical law. One of the major themes in the book is that biology is messy and complicated. That's what makes it so hard.

      Delete
    4. And interesting. If we wanted simple and mind numbing we would just tune in to UD.

      Delete
    5. Larry-- Plant species/genomes are your friends when it comes to evolution of genome size. There is clear evidence that the brassica lineage, for instance, has undergone a series of genome multiplication events over the 25-40 MY since it's divergence with the Brassica/Arabidopsis common ancestor. There is an amazing amount of explanatory potential in that finding alone-- how genomes grow to be so big and with so many apparent genes; how the functional redundancy afforded by genome duplication events affords the opportunity for neofunctionalization and the evolution of novel traits; and for imparting a sense of how unneeded or unwanted allelic copies can become degraded to pseudogene status in fairly short order, leaving nothing left but junk remnants in their wake.

      Delete
    6. Then you need to be able to explain papers such as Whitney et al. (2010) "A Role for nonadaptive processes in plant genome size evolution?"

      Whitney and Garland (2010) "Did Genetic Drift Drive Increases in Genome Complexity?" should also be addressed.

      Of course, simply stating whether there is or isn't a correlation is not very interesting to me. I'd rather know what drives larger (transposable elements, polyploidy) or smaller genome sizes under relaxed or a lack of selection.

      Delete
    7. I agree that genetic drift or other comparably random fluctuations in allele frequencies over time should be the default hypothesis. However, I fail to see how that concession negates anything said in my post. It is perhaps likely that polyploidization events occur at random, but what happens to the genome after the initial event would seem to have evident drivers rooted in adaptive processes through which gene expression levels are fine-tuned in order to adapt to the new genomic context, often through inactivation of loci that may be overexpressed owing to polyploidy and/or deleted entirely, a possibility made possible due to functional redundancy.

      Delete
    8. Yes, I agree with much of what you are saying. I also find plant genome evolution, especially cases of polyploidization, very interesting. I think I interpreted your response in the context of Larry's reply a little too much.

      Delete
  8. Besides the history of actual genome research I would be interested in the history of the idea that the whole (human) genome is functional. Is there a single source or several. I guess the later but are these unrelated? Thus, I am looking forward for something about the influence "God-doesn't-create-junk-fundamentalists", "adaption-doesn't-allow-for-function-biologists", "20,000-genes-are-not-enough-but-there-are-several-layers-of-regulation-epigeneticists", "noise-denying-what-we-can measure-must-have-some-meaning-biologically-undereducated-technologists", "if-you-can't-make-it-in-science-try-science-writeng-framing-scinence-according-to-their-personal-political-preferences-journalists" and "I-do-everything-for-public-attention-editors-of-high-impact-journals".

    ReplyDelete
    Replies
    1. I think I've got all those things covered!

      You'll have to buy a copy to make sure!

      Delete
  9. Here's a prediction.

    Larry Moran, in say 350+ pages, will IANS say that since current technology can't make heads or tails of ncDNA except for a precious few %, then of course the rest of it is junk. What else could it be...

    until new technology says well no its not junk, more like undiscovered higher level command and control mechanisms....

    then Larry will complain that he NEVER said it was you know REAL junk...that was just a turn of phrase...of course the possibility of function was always there....but we just didn't have the tools for it then....but we do NOW.

    Just like those IDiots said...

    ReplyDelete
    Replies
    1. I suspect this sort of ignorance is exactly what prompted Larry to write this book.

      Delete
    2. Steve, how long have you been posting here for? How is it that somebody can be so dense that they would hang around a blog for months making pithy comments without absorbing any information from that blog?

      > Larry Moran, in say 350+ pages, will IANS say that since current technology can't make heads or tails of ncDNA except for a precious few %, then of course the rest of it is junk. What else could it be...

      You have a serious problem with reading comprehension if you think this strawman, creationist bullshit which Larry constantly rails against is going to be the backbone of his argument.

      Delete
  10. > What's in Your Genome: 90% of your genome is junk

    Subtle ;)

    ReplyDelete
    Replies
    1. As a general rule, the author doesn't have the final say in the title. I'm going to try to put the title in the contract and specify that it can't be changed without my permission.

      I'm also going to try and lock in my right of refusal on any cover designs so I don't end up with embarrassing figures/drawing on the cover of the book. (Like the incorrect structure of DNA on "The Deeper Genome.")

      I'm not optimistic about convincing a publisher.

      P.S. I left out the question mark in the title when I first posted my blog post. I've added it back.

      Delete
    2. As a general rule, the author doesn't have the final say in the title. I'm going to try to put the title in the contract and specify that it can't be changed without my permission.

      That's only true in a couple of countries (I'm not sure it's even true in Canada). But since the book is likely made available internationally you could potentially stop publication under an altered title in quite a few places even without explicitly putting it into your contract (in countries like France and Germany a contract stating the opposite - granting a publisher the right to change a title without the consent of the author - would be partially voided even). The same is true for cover designs.

      Delete
    3. Simon, just out of curiosity, how many books have you written and which publishers have you worked with?

      Delete
    4. We worked with a university press to publish our (hopefully first) book. The contract said the press could choose the cover and title. When we disagreed about the cover, though, they did what we wanted after some discussion.

      Delete
    5. Larry, I've written 0 books. But I have acted as publisher for some records when I was younger and as part of that I looked into the legal situation (the way it works internationally is that you have to comply with a boatload of national laws as a publisher, while as a consumer you only need to care about your local laws). There are very few lawsuits based on this part of continental European copyright laws, because European artists generally just get the last word, but are willing to discuss it with publishers first and artists that come from case-law copyright places are generally unaware that they could sue if they feel a change or addition made by the publisher is detrimental to their work. British copyright was first and foremost designed to protect the right of publishers to exclusively sell copies of a work. Continental European copyright was primarily designed to protect creators from publishers. If your publisher makes your book available in Europe, these laws apply as well. I think that this had the biggest impact on movies, where in Hollywood studios usually have final say in the cut - there have been cases where the studio cut didn't get shown in Europe, we got the directors cut as a cinematic release.
      tl;dr: Don't treat getting final approval for title and cover as a concession by your publisher unless they are specifically limited to release your book in a few countries. If I can order their book from a German bookstore, then they have to give you final say.

      Delete
    6. Simon says,

      Larry, I've written 0 books.

      Yeah, that's what I thought.

      You don't know what you're talking about. This has nothing to do with copyright law. Try contract law.

      BTW, my previous books have been published in at least 10 countries (and four languages) that I know about.

      Delete
    7. This has nothing to do with copyright law. Try contract law.

      Most of the legal systems in Europe do not allow an author to waive the right to have the final word on things like cover and title in a contract. Again, that comes from civil law, which recognizes non-transferable rights for authors and one of them is the right to withdraw the right to publish from a publisher when that publisher makes any alteration or addition to the work. In a case where the cover would show an incorrect structure of DNA you'd even have a good case for being granted damages under German law, which holds that an alteration or addition made by a publisher that can lead to damage to your reputation (which such a title design would possibly do) does allow you to force them to stop the distribution and holds them liable for lost profit on sales of the book as well as whatever you lose due that damage to your reputation. I'm aware that this is not a part of Canadian copyright. Nor is it in the US version (and the UK version allows you to waive these rights in a contract, but maintains you have them unless you explicitly waive them). But most books are released internationally and in this case you have grounds for legal action in countries that grant you additional rights.

      Delete
    8. You will quibble about anything, won't you?

      Delete
    9. In this case I thought I was being helpful by pointing out that if your publisher is going to make your book available globally you get to enjoy some rights as the author. It's not something publishers tell authors (and might themselves not be aware of). If you are not optimistic about being granted something that in most of the world is your legally enforceable right, I think it's worth pointing out that that's not something a publisher can do and still put an ISBN on the book and ship it to Amazon France.

      Delete
  11. Good luck! I've been trying to write a book for years. I keep getting sucked into stupid arguments online ...

    ReplyDelete
  12. Ah, I almost forgot: Please try to make it available on Kindle (unless you have an objection to books in that format).

    ReplyDelete
    Replies
    1. I second that! I've run out of room for bookshelves. Gobs of room left on my Kindle app.

      Delete
  13. Who will be your intended target audience? Genome researchers, the general public? Both?

    ReplyDelete
    Replies
    1. The target audience is people like those who read this blog. I'm not going to write a book for the average person who knows nothing about science and I don't intend to dumb down the biochemistry.

      Chapter 1 will cover everything you need to know but some of those things are going to take a bit of effort. You will need to know, for example, that genes have an orientation and you will need to know how transcription is initiated. There will be jargon—you have to learn the meanings of words like chromatin, transcription factors, alternative splicing, open reading frames, transposons, etc.

      Here's part of the Introduction

      Lots of people are writing science books these days. The goal of the average author is to explain science to the average reader who has no scientific education. These authors assume that science is too complicated for their potential audience so they go out of their way to dumb down the science and avoid scientific terms.

      This is a problem, not a feature. We live in a scientifically illiterate society and our goal should not be to cater to those who resist – for one reason or another – learning about science. Our goal should be to teach science to those who want to learn and you can't do that if you oversimplify and avoid difficult concepts.

      Part of the problem here is that most science authors are addressing the wrong audience. The audience they think they're writing for is the scientifically illiterate masses—the ones who are reading the novels on the New York Times best seller lists.

      Well, I got news for those authors, that's not the group who are going to buy your book! The real audience—the ones who are going to read this book and all the other science books—is much more knowledgeable about science than you imagine. They are eager and willing to learn more about science. They read the science magazines and what's left of the science section in newspapers. They watch science shows on television. They read about science on blogs and on Facebook.

      The real audience doesn't want dumbed-down science. They want to be informed and educated. They want to be lifted up, not put down. They know the difference between a gene and an allele or, if they don’t know, they are capable of learning this important distinction. They need to learn it in order to understand modern biology.

      That's the audience I'm writing for.


      ©Laurence A. Moran

      Delete
  14. Good luck with the book. I have been writing one, too (Mutation, Randomness, and Evolution). Maybe we should compare notes. I'm actually working on a section on genome evolution.

    What I would suggest is to establish an objective framework for what's important, based on what are the quantitatively greatest dimensions of between-species diversity, within-species diversity, and intra-genomic heterogeneity. Then, I would set up a neo-Darwinian strawman in which evolution is a process of gradual adjustment to conditions based on selection acting on abundant infinitesimal variation in the gene pool. Then I would go through the examples one by one, discussing evolution, with the end result revealing that, in genomics, we're just in a completely different world than the world of Fisher, Mayr, et al.

    1. roughly a million-fold range in genome size for cellular species
    2. large within-species variation in size in prokaryotes, e.g., 30 % in E. coli
    3. diversity in GC content from 20 % to over 80 %
    4. within-genome structure in the form of repeats
    5. between-species heterogeneity in repeat content

    All of those dimensions can be observed if we look at genomes as an abstract set of sequences, without considering what sequences encode or how they change.

    If we now map the genes on genomes, compare genes within and between species, and relate these to a branching process of evolution, we get

    6. scrambling of genetic maps
    7. genome doublings and segmental duplications
    8. differential gene family evolution by birth and death
    9. Mobile element invasion and propagation
    10. Intercompartmental transfer.
    11. Lateral transfer and the meta-genome.

    If we go through these examples, we find again and again certain departures from the strawman of neo-Darwinism. They are
    * dependence on individual mutations including macromutations (e.g., genome doublings)
    * selection at the level of parasitic elements
    * mutation biases
    * biased gene conversion
    * the combination of drift with differential factors to create patterns that all relate to N, a la Lynch

    ReplyDelete
    Replies
    1. forgot to add, prior to 6:
      6. 200-fold difference in gene number
      7. split genes resulting in variation in gene size

      Delete
  15. Larry, have you considered involving an online community in the writing or vetting of your book? Unlike most prospective authors, you have an online community to draw on.

    ReplyDelete
    Replies
    1. How would that work? Committees can't write books.

      Delete
  16. Larry, it's my pleasure to welcome you to the 21st century and a thing called "wikipedia", an encyclopedia with articles written by an online community. However, group composition is not really at the top of my list of things to consider.

    1. Crowdsourcing knowledge with challenges like
    * What's the best story of an adaptive hypothesis in molecular evolution that achieved popularity and then completely fell on its face?
    * what's the best case of a mutation system that violates the neo-Darwinian doctrine against situation-appropriate mutations?

    If you challenged people to provide references and encouraged some vetting of ideas, this might be a great way to generate useful content.

    2. Release a draft of your book in this forum, one chapter every week.
    * offer prizes for finding factual errors
    * use this as a way to gauge which sections need more work
    * set up an issue tracker (e.g., on github) to track bug reports and feature requests

    3. Consider some way of sharing credit for people who might want to provide expertise or labor. For instance, in a well produced scientific book, there are going to be a lot of custom figures. Maybe you could publish your book as authored by "Larry Moran, with X, Y and Z", where X, Y and Z are people who helped.


    ReplyDelete
    Replies
    1. Thanks but no thanks. I've had enough trouble dealing with reviewers on my previous books. I'm not going to encourage every IDiot to critique my chapters before publication. Besides, there are copyright issues to consider.

      However, I'm happy to observe your experience as you write your book in that manner.

      Delete
    2. OK, so nothing got through. You're still stuck on the misimpression you started with. Got it.

      Delete
    3. Arlin, I don't understand you. What "misimpression" are you referring to?

      1. I'm certainly going to incorporate facts and factoids that I learned from comments on this blog. In fact, I've already put some of them in the first drafts.

      2. I am not going to publish drafts of every chapter and ask dozens of people to act as critics and editors. I know from experience with biochemistry textbooks that this doesn't work.

      3. I'm not going to bring in co-authors for a trade book like this. This is my opinion of what's important and nobody else's. I'm making my own custom figures just like I've been doing for the past 20 years.

      Are you under the impression that most science trade books have multiple authors? Have you seen books by Carl Zimmer with X, Y, and Z or Richard Dawkins and friends?

      Delete
    4. Thanks but no thanks. I've had enough trouble dealing with reviewers on my previous books. I'm not going to encourage every IDiot to critique my chapters before publication.

      Larry, this raises a point I'm curious about (that of course I hadn't thought of, not being an author). I assume you are having/will have people critique the book. Do you at this point have a very definite idea as to who that will be? Will you be trying to balance reliance on trusted individuals who mostly share your ideas and viewpoint with reviewers whose knowledge you respect but who may have different views on some topics? Or is life too short and writing a book difficult enough without inviting contrary views at the review stage?

      Delete
    5. I know who's going to review and critique the draft chapters of my book.

      Will you be trying to balance reliance on trusted individuals who mostly share your ideas and viewpoint with reviewers whose knowledge you respect but who may have different views on some topics?

      I'd love to find a scientist whose views and knowledge I respect but who thinks that most of our genome is functional.

      Do you know of any such person?

      Delete
  17. Larry,

    It's too bad you have removed my comment without leaving any trace of it...

    I know I have been silly but I still believe that your book could be a breakthrough. I have even contacted some of my literary agents from long ago and even the recent ones, just to see if they would be interested in getting your book published. I hope you have at least one literary agent working with and for you Larry.

    ReplyDelete
    Replies
    1. You have no idea how it makes me feel to know that you are trying to help by recruiting an agent for me.

      Delete
  18. Dr Moran, two quick questions. Where can I get one of those Darwin plush dolls, and is Graur's new book worth spending >$100 for a layman?

    ReplyDelete
    Replies
    1. I don't remember where I got Darwin but I have seen it in stores from time to time. Check Amazon.

      I don't think Graur's book is going to be very helpful for the average person.

      Delete
    2. You can get a sample chapter of the book from here: http://www.sinauer.com/molecular-and-genome-evolution.html#sample_chapters .

      Delete
    3. I found Graur's short article helpful:
      http://gbe.oxfordjournals.org/content/7/3/642.full

      "An Evolutionary Classification of Genomic Function"
      Genome Biology and Evolution Volume 7, Issue 3
      pp. 642-645.

      Delete
  19. I hope and trust that a substantial part of the book will be devoted to transposable elements and how awesome they are! :)

    ReplyDelete
    Replies
    1. Yeah, transposons are everywhere in the book. Problem is, it's not easy to explain what they are and how they work.

      I spend quite a bit of time explaining why most transposon sequences are inactive and nonfunctional. I don't think this is appreciated by the average person interested in science. (Or by ENCODE researchers.)

      I also have fun (not!) trying to explain the difference between selfish DNA and Dawkins' version of selfish genes.

      Here's a question. If real, active transposons are functional, not junk, then what about Alu sequences?

      Delete
    2. Do you mean that because Alu sequences can't move around on their own and rely on other transposons to facilitate their proliferation they should be classified as junk?

      I confess that the junk vs. non-junk paradigm doesn't seem that useful to me, especially when it comes to transposable elements. They are so plentiful and diverse, and they can have such a wide range of different kinds of consequences at the cellular and phenotypic level (ranging from benign to helpful to deleterious). Trying to fit even a single class of TE (such as alu elements) into a binary functional vs. junk framework just doesn't seem possible to me.

      Delete
  20. What does Ken Weiss mean when he says "Drift is apparently a mythical or even mystical, or at least metaphoric concept"? See here.

    ReplyDelete
    Replies
    1. It's unclear. The whole series of posts is suffering from the incorrectness of its central premise (Darwin did not propose a deterministic theory - in fact proposing a non-deterministic scientific theory was a key innovation of Darwin and Wallace and this break with a deterministic view of nature had an impact on physics.
      In part III (your link after correcting it leads to part II) Weiss conflates drift with neutrality (drift is the centralized part of population resampling, selection the remainder. In the neutral case the selection part is 0, but there's still a drift part when s!=0).
      Weiss then claims that neutral theory states that a lot of mutations have s=0. This isn't correct - neutral theory does hold that for a large proportion of mutations s=0 is a useful approximation. s=0 is a reasonable null-model and when you fail to reject the null, the approximation of s=0 is close enough to give realistic results. If you want to be precise about this, s is an absolutely continuous variable and thus the probability that s=0 is 0. However the probability that s is within a particular interval around 0 is >0 and neutral theory is about how many mutations are in an interval small enough so that s=0 is a reasonable approximation.

      Weiss then argues that GWAS show that most traits are affected by a lot of different loci and the cumulative effect of many near-neutral substitutions may not be. That argument fails for two different reasons:
      a) GWAS do not directly measure the effect of SNPs, they use linkage to find likely positions of candidate sequences using linkage. Since linkage decreases around a relevant locus, there are often multiple SNPs in close proximity that are correlated with a trait. Furthermore the sheer number of SNPs used in a GWAS means that you have to use Bonferroni or you end up with a lot of false positives. Even if you have a reasonable number of individuals for your GWAS you can end up in a situation where after Bonferroni nothing would be significant. As a result GWAS results are best understood as a method to eliminate loci from consideration, but showing an actual effect requires follow ups, where you limit your test to a smaller number of loci that have not been moved out of contention by the GWAS.
      b) Cumulative effects do not at all lead to a rejection of neutrality for the individual sites. It's very easy to come up with a scenario, where you have two AA sequences and for each of these there are 2 nucleotide sequences (with a synonymous variant in each case). There are cases where all 4 nucleotide sequences are near-neutral, but the 2 AA sequences are under significiant selection. This does not invalidate neutral theory.

      Delete
  21. Good fortune on the creation and finishing and publishing of this book.
    I like the proposed introduction a lot.
    It stresses bilogy is a complicated subject, i say more then physics etc, and yet says the audience is the educated public. educated meaning more then average. I agree that these days there are more smart people in numbers and relative to the previous centuries. 9hope no one calls me a centryist!!)
    There is enough of a sharp public to not have to write it for a high school demographic.
    Enough people can keep up these days on even these subjects.
    (You can quote me for a backpage comment thing if you want. Although i might like to slip in a creationist point) you probably won't however if i judge these things right.
    Anyways its cool to see books made about things thinking creationists care about. BioChem touches a little in these things.

    ReplyDelete
  22. I think I will buy that book as soon as it becomes available.

    ReplyDelete
  23. I'm researching for a conference paper that is due by Monday and would love an expert opinion on this quick question:
    Although RNA's can contain many bases they can be considered a single molecule, but then again the bases are somewhat weakly bonded together. So I'm wondering whether RNA's would truly qualify as "unimolecular" or whether the use of that term is debatable.


    ReplyDelete
    Replies
    1. This is the first I've heard that phosphodiester bonds, or any covalent bonds for that matter, are considered "weak". What do you mean by that?

      Delete
    2. One strand of DNA, unbroken, is a single molecule.

      Delete
    3. I'm pretty sure that Gary was referring to intramolecular base-pairing bonds that may form among complementary segments of a single RNA molecule. If so, those interactions, however weak or how strong they might be, cannot be considered as anything other than unimolecular events.

      Delete
    4. FWIW, Gary's context is that he wishes to push his idea that RNA exemplifies something that he calls "unimolecular intelligence". To quote Gary, "Unimolecular Intelligence: Clues to the origin of intelligent living things are found in rudimentary molecular systems such as self-replicating RNA, which is known to self-learn. Being a single relatively large molecule (as opposed to a number of molecules working together as a system) more accurately classifies self-replicating RNA (possibly similar molecular systems) as a 'Unimolecular Intelligence'". He is having difficulty demonstrating that molecules are intelligent and that RNA systems do not involve multiple molecules.

      Delete
    5. Oh stop your whining N.Wells. I just wanted to make absolutely sure that the word "unimolecular" applies to a RNA polymer.

      And stop misrepresenting the model and theory that does NOT qualify all RNA's as "intelligent" (as per machine intelligence and cognitive science found in the IBM Watson system, intelligent models from David Heiserman, and basics of human cognition from Arnold Trehub).

      One thing for sure is all the hype about scientists rushing to help investigate new insights was a pile of bullshit. The only time that happens is when it feeds biased vested interests. It's no wonder why soon after he arrived for a proper education young Galileo's professors tried to get him kicked out the university.

      I do have to thank everyone for their opinions. I'm now 100% confident that I am using the proper word to describe a single RNA molecule, though I'm still not certain whether the need to replicate previous contents of its code/memory for it to learn new tricks changes things. In either case I'm at least striving to find the proper terminology for scientific concepts that have never been explained before.

      Delete
    6. I think there needs to be a version of Godwin's Law specifically for scientific discussions, i.e. any comparison of yourself to Galileo should immediately shut down a thread.

      Delete
    7. "One thing for sure is all the hype about scientists rushing to help investigate new insights was a pile of bullshit. The only time that happens is when it feeds biased vested interests. It's no wonder why soon after he arrived for a proper education young Galileo's professors tried to get him kicked out the university."

      You still have the impression that scientists need to drop whatever they are doing and investigate every hypothesis put forward by anybody, no matter how ridiculous. If they don't they are by default part of some conspiracy to... well, what I don't know.

      Delete
    8. Honestly John, I'm thankful that I am not another Galileo. With all the whining and complaining about my scientific theory not being a scientific theory and all the academic organizations that beforehand publicly rejected such a thing as possibly being scientific I would have to paddle a boat all the way from Massachusetts to Rome just to be put under house arrest by the Pope for stirring up this much trouble, then have to paddle it and a few additional passengers all the way back home again.

      Delete
    9. Chris are you saying that nowhere in all of academia there is not a single person who has ever received funding or is being paid for making sure that the general public and public schools are getting honest and accurate information needed to scientifically put an end to the ID controversy and related conflicts that millions of dollars a year are being thrown at?

      If you believe what you are suggesting then I have a used 8 foot dingy with a 1/4 inch plywood hull that twice crossed the Atlantic Ocean, which you can have for only $1000 US dollars.

      Delete
    10. Oh and "dingy" should be spelled "dinghy". I built her when I was in my early teens or before (and bad at spelling), but she recently had a fresh coat of paint that strengthened her hull even more. For her age she's not at all dingy looking.

      Delete
    11. No, Gary, I'm saying that scientists are not required to spend their resources investigating every armchair hypothesis put forward on the internet. And not doing so is not any indication of some vast conspiracy. Scientists are not a monolithic entity trying to preserve some ideology. That would be religion. Scientists are highly decentralized and generally critical of each other.

      I don't know where you got this from my post:
      "Chris are you saying that nowhere in all of academia there is not a single person who has ever received funding or is being paid for making sure that the general public and public schools are getting honest and accurate information needed to scientifically put an end to the ID controversy and related conflicts that millions of dollars a year are being thrown at?"

      But since you bring it up, very few scientists (as a % of our total) are actually ever involved in public educational policy or public school curricula. The "ID controversy" is mostly a religious/ideological phenomenon. Nothing in empirical science supports an intelligent designer.

      Delete
    12. Um Chris, what I model is not a religious/ideological phenomenon.

      http://www.planetsourcecode.com/vb/scripts/ShowCode.asp?txtCodeId=74175&lngWId=1

      http://intelligencegenerator.blogspot.com/

      http://theoryofid.blogspot.com/

      If y'all are too busy with your Evolutionary Algorithm based shit then we the taxpayers are best off to save our money and let you fund all your own work, like I have to. Fair is fair...

      Delete
    13. And FYI, this is the four requirement operational definition for intelligence that applies to any system, including RNA based ones. It does not say God-did-it or even Selection-did-it but of course it's only model based science so who in science should even care about that?

      Behavior from a system or a device qualifies as intelligent by meeting all four circuit requirements that are required for this ability, which are: (1) A body to control, either real or virtual, with motor muscle(s) including molecular actuators, motor proteins, speakers (linear actuator), write to a screen (arm actuation), motorized wheels (rotary actuator). It is possible for biological intelligence to lose control of body muscles needed for movement yet still be aware of what is happening around itself but this is a condition that makes it impossible to survive on its own and will normally soon perish. (2) Random Access Memory (RAM) addressed by its sensory sensors where each motor action and its associated confidence value are stored as separate data elements. (3) Confidence (central hedonic) system that increments the confidence level of successful motor actions and decrements the confidence value of actions that fail. (4) Ability to guess a new memory action when associated confidence level sufficiently decreases. For flagella powered cells a random guess response is designed into the motor system by the reversing of motor direction causing it to “tumble” towards a new heading.

      Delete
    14. Gary,

      "Um Chris, what I model is not a religious/ideological phenomenon."
      I wasn't talking about you, but the ID/creationist movement in general. I am not familiar with your theories and computer modeling is not my area of expertise.

      "If y'all are too busy with your Evolutionary Algorithm based shit then we the taxpayers are best off to save our money and let you fund all your own work, like I have to. Fair is fair..."

      I don't know about "Evolutionary Algorithm based shit", but evolutionary theory has been a highly productive theory thus far. Evolutionary biologists have to compete for funding like all other scientists. If you want funding for your ideas. you will have to convince a funding agency that your ideas are worth putting money into, like all other scientists have to do. Fair is fair.

      Delete
    15. Gary,

      "It does not say God-did-it or even Selection-did-it but of course it's only model based science so who in science should even care about that?"

      There is nothing wrong with model based science per se. Computer modeling enters into scientific studies on many different levels. It would be OK if your model said "goddidit", or the flying spaghetti monster did it. They could represent alternative hypotheses. As long as your model was able to distinguish among hypotheses in a unique fashion and is predictive of real world observations according to one or another unique hypothesis, a model can be useful.

      Delete
    16. I am not employed by an entity that receives government funding or flaunt credentials. Therefore I'm just a working class pee-on who works in the private sector that only gets to pay and pay and pay so that others who have the right connections can spend and spend and spend.

      In comparison to the models I have been developing the Darwinian models are obsolete 18'th century generalization based antiques. But it seems as though you would have had to model both to know why the methodology I now use antiquates what academia regularly gets millions of dollars to develop and teach. Darwinian algorithms cannot even predict whether the system being modeled is intelligent or not, which makes all the "evolving intelligence" with then a waste of time and money.

      To be fair I should be given as much of a chance at receiving funding as someone who has a university grant writers and all else, but in reality that is not how the system works. Even the Templeton Foundation dissed me by directing me to BioLogos for a micro grant to write articles to promote Evolutionary Creationism. They claim to support science yet those who win their awards only need arguments from ignorance or religious tripe.

      If you want to be fair about it then university researchers must all be rejected by the NSF, just like I have to be.

      Delete
    17. Charles Darwin wasn't born until 1809. He published the first draft of The Origin of Species in 1859. The 1800's were the *nineteenth* century.

      If you're having this much trouble with basic arithmetic, Gary, could that explain some of your problems getting grant money?

      Delete
    18. Word has it that Charles Darwin was not the first to describe "selection" and where Arab naturalists are considered it's 6'th century thinking. But 19'th century is back enough it time to get my point across.

      Delete
    19. Just to be on the safe side I just checked dates and it looks like at least 9'th century thinking:

      https://en.wikipedia.org/wiki/Al-Jahiz

      and/or:
      https://en.wikipedia.org/wiki/Kit%C4%81b_al-Hayaw%C4%81n

      With all the controversy over the exact date and who was really first just pick a number from 0 to 19 and I'm OK with it.

      Delete
    20. Gary,

      Actually, you are being treated as fairly as can be expected. Getting money to do research is highly competitive. I have only experience in mainstream science, meaning my proposals have been with access to a fairly well equipped lab and with the infrastructure of a university, i.e. the usual situation for applying to a federal/state/international/corporate type grant.

      "I am not employed by an entity that receives government funding or flaunt credentials. Therefore I'm just a..."

      One thing you need to understand, Gary, is that most scientists are working class peons as well. It's our job. Most of us aren't getting the grants, we are working for others who get the grants. And all of us, whether we are primarily getting grants or primarily carrying out those grants, we are all working hard and doing all the rest of things people do, like raise families and try to find time for hobbies and other interests in life. And for those people getting the grants, they get by on their own merit and what grant money they bring in. Whether the 'entity they are associated with' gets grant money is largely irrelevant. The university they work for gets a cut of the money that successful scientists bring in. If you think science is some cake job then you have no idea what this is all about. None.

      "In comparison to the models I have been developing the Darwinian models are obsolete 18'th century generalization based antiques. But it seems as though you would have had to model both to know why the methodology I now use antiquates what academia regularly gets millions of dollars to develop and teach."

      The models used by science today are not "18th century based antiques". If your methodology antiquates modern evolutionary theory, then write a grant and get the resources you need to establish your case. I must repeat: there is no vast conspiracy against you and your ideas. Convince some funding entity you have ideas worth advancing.

      "Darwinian algorithms cannot even predict whether the system being modeled is intelligent or not, which makes all the "evolving intelligence" with then a waste of time and money."

      There is ZERO and I mean ZERO evidence that a natural organic system requires some outside intelligence to sustain it and make it work. ZERO.

      !OK, I want to be absolutely clear here that there is no credible evidence that an intelligent force of any kind intervened at any point in the history of the Universe to produce anything we see.!

      That is my starting hypothesis.

      If you have models/algorithms that can uniquely separate my starting hypothesis from any other hypothesis in a reliable, scientifically rigorous manner, or even a reasonable expectation it could do so, you would be competitive for many types of grants.

      Delete
    21. "There is ZERO and I mean ZERO evidence that a natural organic system requires some outside intelligence to sustain it and make it work. ZERO."

      I can tell that you did not even look at the models and theory. That says a lot about your lack of objectivity.

      I also know plenty of scientists who need funding, some of them PhD's. The issue here are the education related entities who are already being paid to keep up with the times being asleep at the wheel.

      Delete
    22. Yeah yeah Gary, you're invoking Galileo's gambit. 'Everybody is against me', 'I'm just a poor working class peon', 'scientists only have to hold up their hands and the peon pays their gazillion dollar salary', 'I work my ass off to pay for the scientists mansions' etc.

      Thing is Gary, and this has been mentioned to you a lot of times, YOU need to provide evidence your model is working, before grant organizations will consider handing out the money. Your only argument is invoking GG (how ironic?) and that won't work.

      Delete
    23. Go reread what I said Ed. It does not matter whether an "individual" has worthwhile ideas, federal and other grants grants are simply not allowed to be given to "individuals" just because they have worthwhile ideas. And considering how the model/theory qualifies as ID even the Templeton Foundation rules specifically state that such work cannot be funded. It's not supposed to be science, and that's that. I'm not even welcomed to publish a paper in a major journal, it is supposed to be rejected before even reading what it says.

      You and others seem to have no idea how hypocritical this situation actually is. It's a historic screw-up.

      Delete
    24. And please excuse typos. After rushing a conference paper for the Blyth Institute on the Cognitive Origin of the Scientific Method that is due this week (officially today but still have a little more time) I ended up deliriously tired and had to rush everything.

      Delete
    25. Gary, I'm not employed by any university, and I get papers published regularly in small journals that are well respected in my field. I don't know about getting grants, but as far as publishing goes, your problem is the paper's content, not your lack of formal academic affiliation.

      Delete
    26. Gary,

      "That says a lot about your lack of objectivity."

      No, it says a lot about what I consider evidence. Models are not evidence. Eventually models have to have some real world application where you can test the model and accumulate evidence. It is not a lack of objectivity to recognize this.

      Delete
    27. If you read Thomas Kuhn carefully, one of his main points is that scientists don't dump the prevailing paradigm until it has reached the limits of its usefulness. Then they go through a period of frustration until a new paradigm breaks the impasse, after which they happily go on testing the new paradigm.

      Right now, I don't see any of the standard paradigms in biology or the historical sciences breaking down. Geologists seem to be still testing and refining plate tectonics; biologists don't seem to be anywhere near finished exploring all the ramifications of genomics; abiogenesis has even had a breakthrough with the RNA world.

      So, I'm wondering, Gary, where your models and theory would fit in a paradigm shift. Where do you see scientists "stuck" in their research that your theories would be the key to moving ahead?

      Delete
    28. Who the hell is talking about dumping the prevailing paradigm other than you hoary?

      You are a dumbass.

      Delete
    29. And Chris, if you are unable to tell the difference between science and religion then you are a dumbass too.

      Spare me your pompous kick in the head.

      Delete
    30. bwilson, my problem boils down to pompous assholes who shove words in my mouth while talking about "papers" and theory that they never even read.

      Delete
    31. Gary--

      You've been talking about your model and your theory. Let me put it another way. How do you think your model and your theory would be useful to scientists who are currently using the prevailing paradigm? How would your model and theory lead to new breakthroughs and discoveries?

      Delete
    32. Gary,

      "And Chris, if you are unable to tell the difference between science and religion then you are a dumbass too."

      I am able to tell the difference between science and religion.

      "Spare me your pompous kick in the head."

      I am not kicking you in the head. The points I brought up are basic.

      At your theoryofid website you say your theories generate scientifically testable predictions. Can you provide one as an example?

      Delete
  24. Then along with what was said in a biochemistry forum, there is no debate that ssRNA is "unimolecular".

    This is the first I've heard that phosphodiester bonds, or any covalent bonds for that matter, are considered "weak". What do you mean by that?

    I said "bases are somewhat weakly bonded together" because from what I know the base to base bonds are weaker in comparison to the ones forming each base, which normally stay together when a strand is broken.

    ReplyDelete
    Replies
    1. Then along with what was said in a biochemistry forum, there is no debate that ssRNA is "unimolecular".

      Not the whole story, though the issue is not one to get too worked up over. The xNA backbone is held together by covalent bonds. These, shading into ionic, are conventionally the kinds of bonds that hold 'molecules' together.

      Complementary bases in dsxNA are paired by weaker hydrogen bonds. You can have dsXNA in a single molecule. If it forms a hairpin structure, it's still one molecule but with a dsRNA stretch; if you cut the backbone at the turn, it's 2 (but doesn't just come apart). Likewise, 2 molecules of dsDNA transiently can becomes 4 molecules when topoisomerase acts or there is a double-strand break. Unless it's in a prokaryote or a mitochondrion.

      Delete
  25. With apologies to Charles Darwin:

    “It is interesting to contemplate an entangled genome, with many DNA sequences of many kinds, with active genes transcribing, with pseudogenes decaying, with various transposable elements flitting about, and to reflect that these elaborately constructed forms, so different from each other, and dependent on each other in so complex a manner, have all been produced by laws acting around us...”

    ReplyDelete
    Replies
    1. With apologies to TIME magazine:

      http://content.time.com/time/specials/packages/completelist/0,29569,2046823,00.html

      Delete
  26. OT: For the last few days, looking at Sandwalk, the Recent Comments widget displays no recent comments along the left side of the front page. Is anyone else having this problem? I can see new comments among the comments once I open each thread.

    ReplyDelete
    Replies
    1. For me this has always been inconsistent - I sometimes got the recent comments and sometimes didn't, but in the last few days I didn't get it on the front page and the last time I had it come up in a thread has also been a while.

      Delete
    2. I added a new widget. I don't know why the old one stopped working.

      HTH HAND

      Delete
    3. The reason my third party widget stopped working was because Blogger switched my blog URL from "http://..." to "https://..." on May 10th.

      Blogger didn't think it was important to let us know about this change.

      Blogger doesn't seem to care very much about comments. It doesn't have its own widget for comments and it refuses to address complaints about the lack of an editing function in comments and the inability to format them.

      On the other hand, there are some very good features on Blogger so I'll be staying here for a while.

      Delete
    4. Glad to see "recent comments" working again.

      Delete
    5. The new widget needs work. It can't seem to handle punctuation, and doesn't identify to which article the comments belong. My 2 cents.

      Delete
    6. @lutesuite,

      Thanks for your 2 cents.

      If you can find me one that works better, I'll gladly install it. I tried five different ones and this one is the only one that works.

      Delete
    7. Oh, no! Recent comments widget becomes another example of "New! Improved! Worse!" So common, especially with computer things. (Thanks for trying alternatives.)

      Delete
    8. One other comment about comments:

      Do others also find that after a certain (large) number of comments has been reached on an article, new comments will show up in the widget, but not in the actual comment thread below the article?

      (This occurs in all of the web browsers I've tried, including Internet Explorer, Firefox, Google Chrome, Safari, Opera, and Vivaldi, on my work PC, home PC, and MacBook Pro laptop.)

      Delete
    9. I've seen this problem, so I go to the bottom of the comment, click on "Load more," wait for the rest of the comments to load, and then do a search on some distinctive phrase from the comment. It works, but is awkward, and seems a good reason to abandon a long thread.

      Delete
    10. I'm not seeing "Load more." Where is that?

      Delete
    11. Bottom of the page. Though I think it just says "Loading".

      Delete
    12. I've seen both "Load more" and "Loading." I don't know why. Much about the comments remain mysteries to me.

      Delete
  27. Larry,

    I'm just curious; how are you going to structure your book? Do you have a synopsis in mind?

    Are you going to quote as many as possible sources that support your idea of 90% mammal/human genome being junk? Is that your main goal?

    Or, are you going to challenge the research, which comes out pretty much every day, that in so called "junk DNA" there are possible solutions to such diseases as cancer, Parkinson's, multiple sclerosis, heart disease, diabetes and many, many more?


    Are you going to challenge those researchers as being wrong?

    Are you going to tell those researchers to stop digging in so called "junk DNA" because you are sure it is just useless junk?

    ReplyDelete
    Replies
    1. One of the main goals is to present all the evidence against junk DNA ( e.g. ENCODE) and show why it has been misinterpreted. This leads to an extended discussion of science reporting and why the general public has been mislead on this issue.

      The section on medical relevance is only a few pages. It's very easy to explain why mutations causing medical diseases often fall into functional noncoding DNA since the opening chapters explain the basic biochemistry. It's also easy to explain why mutations in very important functional regions never show up as genetic diseases ... because they are lethal long before birth.

      My message to researchers is to keep digging in the junk DNA but learn how to behave as proper scientists by being skeptical of your results and don't make claims that you can't support. Always keep the big picture in mind before making grandiose claims based on a tiny bit of functional DNA.

      Of course I'm also going to explain all the evidence in support of massive amounts of junk DNA. This is an important part of the book since there are a lot of people out there who don't know about this evidence based on 50 years of research. They think the idea of junk DNA is based on LACK of knowledge instead of real data. I'll try and correct their own lack of knowledge that leads to this false impression.

      I don't expect to convince anyone whose ignorance is based not on science but on religious faith. That kind of stupidity is immune to logic and reason as you have demonstrated repeatedly by your comments.

      Delete
    2. It's good you're emphasizing the large numbers of spontaneous abortions that eliminate mutants. This point doesn't seem to enter the public discourse at all.

      (Of course, scientists know about it. But I've seen science-defender versus creationist debates where the creationist smugly asks, where are the mutants-- and the science defender just concedes the point.)

      Delete
  28. One of the main goals is to present all the evidence against junk DNA ( e.g. ENCODE) and show why it has been misinterpreted. This leads to an extended discussion of science reporting and why the general public has been mislead on this issue.

    I thought you were going to present ALL THE EVIDENCE FOR JUNK DNA and AGAINST ENCODE?

    As far as I know, ENCODE is not backing out. I know someone on the upper team and they pretty much stick to 80% functional genome with the high possibility of the whole genome being functional close to 100%.

    So, it appears that it is you, and a couple of other guys that ENCODE made look bad with your predictions.

    What are you going to do if in 3-5 years 50% of human genome will turn out to be officially functional? Are you going to take it ALL back and apologize? I truly doubt that.

    The section on medical relevance is only a few pages. It's very easy to explain why mutations causing medical diseases often fall into functional noncoding DNA since the opening chapters explain the basic biochemistry. It's also easy to explain why mutations in very important functional regions never show up as genetic diseases ... because they are lethal long before birth.

    Why few pages Larry? Don't you have a free subscription to most medical journals? There is overwhelming evidence that the key to treating the most common disease may and possibly is located in what you and your buddies believe to be "junk DNA". I can post tens of links right now.

    My message to researchers is to keep digging in the junk DNA but learn how to behave as proper scientists by being skeptical of your results and don't make claims that you can't support. Always keep the big picture in mind before making grandiose claims based on a tiny bit of functional DNA.

    This part I don't get Larry. I think you will have to explain it to me.
    Why, as a scientist, should I be sceptical of the results I have that, for example, prostate cancer regulation region appears to be in the region of DNA that you, and your buddies claim to be junk? Larry, please be as clear as possible because I personally don't know one single scientist that would obey your command. No way!I'm not speaking for myself right now.

    Of course I'm also going to explain all the evidence in support of massive amounts of junk DNA. This is an important part of the book since there are a lot of people out there who don't know about this evidence based on 50 years of research. They think the idea of junk DNA is based on LACK of knowledge instead of real data. I'll try and correct their own lack of knowledge that leads to this false impression.

    That is fine Larry but many of my colleagues and myself included will criticise your book. So, if I were you, I would make sure that your claims are up to date. That is all.

    I don't expect to convince anyone whose ignorance is based not on science but on religious faith. That kind of stupidity is immune to logic and reason as you have demonstrated repeatedly by your comments.

    I'm going to restrain myself from commenting on this issue Larry because it is pointless. I leave this to the public opinion as to who is doing what and on what evidence or faith. I will let the insightful minds to decide this matter...

    Unfortunately, there aren't many of those today...

    ReplyDelete
    Replies
    1. Is this the first time that Eric has claimed to be an actual working scientist, and apparently a biologist? Just wondering.

      Delete
    2. I think it's not the first time.

      Delete
    3. Did anybody believe him that time?

      Did the LA Lakers reach the play offs?

      He also poses as an entrepreneur, handing out money to fund projects with the goal of committing mass murder.

      Eric's a person of many faces.

      Delete
    4. Already early on I guessed Eric is probably a person who's (hopefully) in frequent contact with men in white coats, and gets his one hour of daily internet time at some institution where he lives.

      Delete
    5. I know someone on the upper team

      Would you like to give us the rosters of the "upper" and "lower" teams?

      By the way, don't know if you happened to notice, but one of the ENCODE team has commented frequently on this blog agreeing with Larry. I think this trumps you "knowing a guy."

      Delete
    6. Already early on I guessed Eric is probably a person who's (hopefully) in frequent contact with men in white coats, and gets his one hour of daily internet time at some institution where he lives.

      Yes. Lab technicians who think too much of themselves like Mikkel Rumraket Rasmussen because they "touched" the real science work under me whether they like it or not.

      Delete
  29. Are you planning to review some of the knock-out experimental data in your book?

    How about fugu and such? Are you going to mention any of that "junk DNA" anomaly?

    If you don't submit your book for publishing by the end of the year, there may be some experimental results of knock-out mice and some plants that you may find very interesting...

    ReplyDelete
  30. Larry,

    Off topic.

    I hope you don't remove it.

    The company I'm part of has a little bit of money to spare on real, experimental research. The board of directors is very, very particular about where the money should go. If you had a real experiment model in mind to prove your "junk DNA" theory, and if it wasn't very costly and very long, they may go for it. Well, it is worth trying- let's put it this way.

    If you had such an experiment in mind that would definitely prove your point and at the same time made ENCODE look like amateurs, they just may go for it. Mind you, they are very careful with spending the foundation and the company money, but one of the board members apparently used to be a biochemists or something like that and he apparently have spoken (critically or not I don't know) publically about ENOCODE.

    Anyways, do you have a dream plan for an experiment that is going to exonerate not only you, but possibly all those losers who made predictions about junk DNA?

    I could submit a proposal on your behalf.

    ReplyDelete
    Replies
    1. What company is this? What is your name?

      Delete
    2. Haha. Why do I know in advance you will not receive an answer to either question John?

      Eric, the experiments suggesting non-functionality of a considerable percentage of genomic DNA have already been done. Now, you get out there and search for functional elements (there are thousands upon thousands yet to be discovered, undoubtedly). If and when you have reached a % threshhold that contradicts Larry's ideas, you report back here and rub his nose in it (be sure you publish in peer-reviewed venues first, mind you). We will wait.

      Delete
    3. Eric,

      You and ENCODE need the money to prove your hypothesis that >10-12% of the genome is functional. It's youse guys that should be applying to the magical company you are talking about. Or to existing granting agencies.

      Out of curiosity, can you provide a link to the company you are a part of and their grant application procedure?

      Delete
    4. Eric,
      I know someone who needs some research done. His name is Perry Marshall. He has a hypothesis that the human genome was originally programmed to evolve through self-modifying code. He needs someone to find the part of the genome that is in charge of re-writing the rest of the genome, and figure out how it works. You can discuss this with him on CosmicFingerprints.com/blog

      Delete
    5. What company is this? What is your name?
      Will knowing the company name change your view on the issue?
      If yes, say why.

      Delete
    6. Eric, the experiments suggesting non-functionality of a considerable percentage of genomic DNA have already been done. Now, you get out there and search for functional elements (there are thousands upon thousands yet to be discovered, undoubtedly). If and when you have reached a % threshhold that contradicts Larry's ideas, you report back here and rub his nose in it (be sure you publish in peer-reviewed venues first, mind you). We will wait.

      Why wait? If you are so certain about your beliefs, why don't you reveal your real name and, like Larry did, make a commitment to your beliefs....

      Delete
    7. Eric,
      I know someone who needs some research done. His name is Perry Marshall. He has a hypothesis that the human genome was originally programmed to evolve through self-modifying code. He needs someone to find the part of the genome that is in charge of re-writing the rest of the genome, and figure out how it works. You can discuss this with him on CosmicFingerprints.com/blog


      All I can say is reveal your name... Larry, Harshman, and many others have committed themselves to their believes; just like the judge Graur said; "...if ENCODE is right, evolution is wrong..." you need to commit to something or you will be ignored...

      Delete
    8. @ Fair Witness,

      Perry Marshall doesn't need research funding. He needs a brain transplant.

      Delete
    9. @lutesuite: I agree. But after watching James V Kohl, another crank, drive Marshall nuts with stupid comments on his blog, I thought it would be entertaining to sic Eric on him.

      Delete
    10. Eric, Nobody believes you're a biologist or that you company exists. I was just giving you a chance to come clean. I was inviting you to admit there is no such company.

      Delete
    11. Eric says: If you are so certain about your beliefs, why don't you reveal your real name and, like Larry did, make a commitment to your beliefs....

      SRM are my initials and my name is Shawn. What is your name Eric? And no I won't "make a commitment to my beliefs". Religious people like you make commitments to beliefs, scientists and rational people do not.

      Delete
    12. Excellent job Eric. The science defenders in this forum now look like they need to be sent back to school.

      Delete
  31. It looks like the book "What's in Your Genome?: 90% of your genome is junk." will need a new title:

    What used to be dismissed by many as "junk DNA" is back with a vengeance as growing data points to the importance of non-coding RNAs (ncRNAs) -- genome's messages that do not code for proteins -- in development and disease. But our progress in understanding these molecules has been slow because of the lack of technologies that allow the systematic mapping of their functions.

    Now, Professor Benjamin Blencowe's team at the University of Toronto's Donnelly Centre, including lead authors Eesha Sharma and Tim Sterne-Weiler, have developed a method, described in May 19, 2016 issue of Molecular Cell, that enables scientists to explore in depth what ncRNAs do in human cells. The study is published on the same day with two other papers in Molecular Cell and Cell, respectively, from Dr. Yue Wan's group at the Genome Institute of Singapore and Dr. Howard Chang's group at Stanford University in California, who developed similar methods to study RNAs in different organisms.

    Of the 3 billion letters in the human genome, only two per cent make up the protein-coding genes. The genes are copied, or transcribed, into messenger RNA (mRNA) molecules, which provide templates for building proteins that do most of the work in the cell. Much of the remaining 98 per cent of the genome was initially considered by some as lacking in functional importance. However, large swaths of the non coding genome -- between half and three quarters of it -- are also copied into RNA.


    https://www.sciencedaily.com/releases/2016/05/160519120935.htm

    ReplyDelete
    Replies
    1. Those papers are about mapping RNA-RNA interactions.

      This has nothing to do with the junk DNA and how much of the genome is functional question.

      Delete
    2. Calling all the functional RNA coding regions "junk" is a childish way of trying to make it seem like you won.

      Delete
    3. Have you actually read the papers? I read them when they came out, the press release you are citing I see for the first time.

      There is literally nothing about function there.

      Delete
    4. Read to material that came from the University of Toronto, which says the exact same thing "large swaths of the non coding genome -- between half and three quarters of it -- are also copied into RNA.":

      http://www.thedonnellycentre.utoronto.ca/news/shedding-light-%E2%80%98dark-matter%E2%80%99-genome

      Along with all the other evidence of function in the noncoding regions of the genome it's best to give up now, before making yourselves look even more childish.

      Delete
    5. When you are making people wonder what is more stupid -- press releases or you -- you should know that this is not a conversation you should be part of

      Delete
    6. Hey Georgi seeing how you have plenty of money or something I need $31.50 to take a look at the paper.

      Delete
    7. Replied

      Also, it's worth recalling this exchange from 5 years ago:

      http://www.ncbi.nlm.nih.gov/pubmed/20502517
      http://www.ncbi.nlm.nih.gov/pubmed/21765801

      You might want to look at the authors' lists of those papers

      Delete
    8. Papers!

      If the police bash down my door and arrest me for theft of scientific materials then I'll have to blame you!

      A quick scan shows that they are discussing the RNA methods only. I'll have to spend some time going through them for more detail. I'm finding this very interesting.

      The estimate for the percentage of the genome that codes for RNA's appears to have been added to the press release only. Normally I would not take it overly serious but in this case it's a more reliable source than usual.

      Delete
    9. A quick scan shows that they are discussing the RNA methods only.

      Precisely.

      The estimate for the percentage of the genome that codes for RNA's appears to have been added to the press release only.

      See above

      Delete
    10. The links above are more or less agreeing with my point all along, which is it's too early to have a reliable estimate:

      We conclude that the totality of the evidence strongly supports pervasive transcription of mammalian genomes, although the biological significance of many novel coding and noncoding transcripts remains to be explored.

      The estimate given in the press release for half to three quarters of our genome is copied into RNA is believable. Claiming what Larry proposes by saying "90% of your genome is junk" is still in my opinion a very bad idea that is doomed to fail. Saying "50% to 25% of your genome is junk" is a safer bet but that does not consider the tethering of nucleosomes/histones where it's then like suggesting that a boat does not need to be roped to a dock or other boats to prevent it from floating away.

      Delete
    11. Georgi Malinov,

      What's your view of the research that has recently been published by more than a few science magazines on the subject of "junk DNA" being the ocean of regulatory functions to unknown areas of science?

      Do you think that your commitment and Larry's is going to stand for a long time?

      I take bets... Are you interested?

      How about this: If in 2 years nobody wants to publish Larry's book, I will sponsor it, but you will write all the supporting bs, provided Larry is okay with that.

      Are interested?

      Delete
    12. What matters, in decreasing order of importance:

      1) Mathematical results
      2) Laws of physics
      3) Data
      4) Primary literature
      ...
      ...
      n) Various secondary, tertiary, and other higher orders sources

      Delete
  32. Okay people,

    Let's talk science!

    How do we prove the guided evolution? Where do we start?

    On the other hand, how do we prove that guided evolution didn't happen?

    I'm really looking forward to this scientific discussion...

    ReplyDelete
    Replies
    1. Let's talk science!
      Yeah!

      How do we prove the guided evolution? Where do we start?
      The ID movement already proposed a hypothesis that only needs to be tested to be true by a testable scientific theory, which I just so happen have all set to go:
      http://theoryofid.blogspot.com/

      I'll soon be improving the wording to make the theory more precise and also cover the cognitive origin of the "scientific method" but it's still a good start towards explaining how "guided evolution" works.

      Delete
    2. When Eric is involved, science is only an incidental part of the conversation. But, being something of an idiot at times, and having work I'd rather avoid for a while, I'll respond.

      I personally wouldn't start by trying to prove or disprove whether guided evolution happens. I'd start by trying to explain how the diversity we see could arise. I would learn about the age of the earth and the rock layers in it, patterns of similarity and difference over time (looking at fossils) and place, population genetics including both selection and drift, the wonderful biochemical diversity within and between cells. I'd wonder if the processes I know about can produce that diversity. (Looks like yes, though we always have more to learn.)

      Thinking about the hypothesis of guided evolution, I'd have two main sets of questions. First, do we need this complication? It doesn't seem we do.

      Second, what predictions would guided evolution make? If it were true, how would it work, when would it work, what would it accomplish? How would its results differ from the patterns we see? Who or what does the guiding, and what evidence do we have for that?

      We can't falsify the guided evolution hypothesis until we know what it predicts, and that's not at all clear.

      So over all, I'd dismiss the hypothesis is an unnecessary complication, an add-on to processes we already know about. And I wouldn't seriously try to falsify it until I knew what it predicts.

      So if you want to get into a discussion of falsification of guided evolution, start by predicting what it would do that is different from what unguided processes do.

      Delete
    3. Some prediction(s):
      The combined knowledge and behavior of all three intelligence levels guides spawning salmon of both sexes on long perilous migrations to where they were born and may choose to stay to defend their nests "till death do they part" from not being able to survive for long in freshwater conditions. Motherly alligators and crocodiles gently carry their well guarded hatchlings to the water, and their fathers will learn to not eat the food she gathers for them. If the babies are scared then they will call and she will be quick to come to their aid and let them ride on her head and body, as they learn what they need to know to succeed in life. For humans this instinctual and learned knowledge has through time guided us towards marriage ceremonies to ask for "blessing" from a conscious part of us that our multicellular intelligence level (brain) may be able to sense coming from the other intelligence levels we cannot directly experience, which at the genetic intelligence level has for billions of years been alive, and is now still alive inside of us.

      Delete
    4. The trouble is, Gary, that natural selection (including kin selection) would explain behavior of the salmon, and of the alligators to the extent what you've written is true.

      Therefore, these predictions don't help distinguish guided evolution from unguided evolution.

      Delete
    5. Darwin's theory by natural selection does not predict or explain how the guiding multilevel intelligence mechanisms work. It's useless for predicting whether there is a guiding intelligence, emergent from the behavior of matter.

      Delete
    6. Gary, natural selection doesn't explain your ideas, but at this point it's not clear that that's a problem, because it's not clear that your idea of multilevel intelligence is true. If, some day, your idea is well supported, reconciling it with natural selection (and drift) will be an issue, but right now it's not.

      Delete
    7. Unguided evolution would result in this being true:
      Salmon would squirt out their eggs in the ocean then let the other fish eat them. Alligators and crocodiles would eat their young. Humans would be "meat robots" that have no need for marriage ceremonies and discard their young soon after birth.

      My theory is very true. All that has been discovered over the past couple of decades is all evidence for it, none against it.

      Delete
    8. And I must add: If I have no problem showing what guided and unguided "evolution" looks like then you should have had no problem doing the same, otherwise the theory you are making predictions from is useless for basic concepts like this and you should be searching for a better one.

      Claiming that a theory you and others never even bothered to test is not well supported is a brush-off. The only thing accomplished by that is the giving of the "scientific community" a bad reputation for being hypocrites that prefer to forever test an antiquated theory. Expecting me to do all that for you is academic laziness, another demeaning brush-off.

      Delete
    9. First, sorry for using this thread to argue against Gary. I'll stop after this.

      Gary, your assertion that your not-a-theory is true does not make it so. You are confusing making assertions with presenting evidence.

      You have not documented the existence of “molecular intelligence” - you have merely asserted it, without providing operational definitions so that other people can figure what it is and how to measure it.

      Your “predictions” are not logically derived from your ideas - you are once again merely making assertions. You are also using bad and pointless "examples" to assert that parental devotion is expected or inherent. For instance, salmon are bad examples of parental devotion because most salmon spawn and die fairly promptly rather than "defending their young". However, the larger problem is that your examples are pointless because a great many animals provide no parental care whatsoever, and simply cast their eggs or babies to the fates.

      In contrast, evolutionary theory offers perfectly good (and testable) explanations for why salmon ascend streams (because minimizing predation pressure on the young results in greater reproductive success), why crocodilian mothers do not eat their young (although crocodilians can be cannibalistic, mothers do not eat their own young, because protecting them and not eating them increases their reproductive success). Old ideas about k selection explain human reproductive and parental strategies just fine.

      Delete
    10. Drats, the brown-noser found me!

      The operational definition for intelligence and information I provided in the .pdf for theory I linked to above is more than enough to model all the levels of intelligence it covers. It's wonderful for systems biology related work. Anyone who needs more than that from someone who gets no funding at all is either new to science or just being a biased creep, like N.Wells needs to be.

      Here's a direct link to download the pdf file of the theory:
      https://sites.google.com/site/theoryofid/home/TheoryOfIntelligentDesign.pdf

      And the associated models that go with it:
      http://intelligencegenerator.blogspot.com/


      Delete
    11. Correction: for discussion of reasons for salmon migration, see e.g.
      McDowell, 1997, in http://www.webpages.uidaho.edu/fish511/Readings/Readings%202010/McDowall%201997%20review.pdf
      Gross et al., 1988, Science at http://labs.eeb.utoronto.ca/gross/Grossetal1988.pdf
      Bloom and Lovejoy, 2014, at http://rspb.royalsocietypublishing.org/content/281/1778/20132081
      Phillis, 2014 at summit.sfu.ca/system/files/iritems1/14549/etd8634_CPhillis.pdf
      Kinnison and Hendry, in Hendry and Stearns, 2014, Evolution illuminated

      Delete
    12. Unguided evolution would result in this being true:

      Salmon would squirt out their eggs in the ocean then let the other fish eat them. Alligators and crocodiles would eat their young. Humans would be "meat robots" that have no need for marriage ceremonies and discard their young soon after birth.


      Nothing whatever in Darwin or any other work of evolutionary biology that I've read would require any of this. It's complete nonsense. Sorry, Gary, but since you haven't cited a valid prediction of evolutionary theory, you haven't conducted a valid falsification.

      Delete
    13. In unguided evolution, genes of individuals who leave more offspring become more frequent in the populations. Animals within a species vary in how much care they give their offspring. In some cases, giving more care results in more offspring surviving and reproducing. In those cases, genes related to caring for offspring will increase in the population. In following generations, parents still vary in how much care they give and the process is repeated. Parental care can evolve in unguided evolution.

      Delete
    14. When Eric is involved, science is only an incidental part of the conversation. But, being something of an idiot at times, and having work I'd rather avoid for a while, I'll respond

      Well bwilson295, one thing I love about this blog is that I get to talk to a lot of "bigmouth scientists" or as my 12 year old son calls them the "chameleon scientists"-because when they are cornered, they appear as other people with the same IP.

      They all pretty much have one thing in common; they think they know something 100% and anyone who questions this is an idiot.

      Let me use an example:

      Humans and bananas share about 50% of DNA. While this may or may not be very surprising, there are obvious problems unless bwilson911, chris b. and other critics of my posts are not humans.

      Well, the problem is obvious, because neither humans nor bananas look not even close to 50% of their 50% identical DNA. They do not resemble each other at all...though some might question that as well..

      I know that "The Darwinian Church" has many theories that try to explain it, but I don't buy their shit. No way.

      All I want to know, with the scientific knowledge that Darwinists claim to have, how to tweak the banana genes to make it look like a human which, I'm sure "the big science" will deny by adding billions of years of random, blind processes that figured it out how a banana became mobile with legs and then it spoke...

      This is nonsense.

      All I want is how to tweak the banana genome to look at least like a nose... and not a banana. Forget it. I want to know how to tweak the banana DNA that it would still function, but it would not be a banana...

      Can you tell me how..? Bwilsons911, judmars, Nwells's?
      I have a privilege and an access to more than few labs in the world. I have access to more than few scientists in the world. I have a limited budget, but I have foundations that seem to have to spent their money or they are going to lose it.

      So, there are opportunities there...
      What scientist wouldn't like to prove his or her beliefs by experimentally proving them? Give me one reason "why"!!!

      Design an experiment that makes sense and will submit it.

      If it is logical, I will forward it to the committee. They are picky all right, but they have scientist of both side on the board. They've rejected my experiments for being "too flamboyant"(like mine), so the respected scientist should get a hearing aid at least...

      Delete
    15. N.Wells: Correction: for discussion of reasons for salmon migration, see e.g.

      None of the papers presented a modeling method for experimenting with the cognitive mechanisms that guide the animals in question.

      It might also be more reproductively successful for all salmon to stay in the ocean, instead of taking a long usually suicidal journey back to where they were born. The easy answers from Darwinian theory is causing you to assume things that could very well be false.

      Delete
    16. Well, my prediction comes true, Eric. And no, even if 50% of the DNA of bananas and humans is identical (I doubt that), it doesn't follow that we would look 50% alike and it certainly doesn't follow that we could tweak a banana genome to make bananas look human. Where do you come up with these things?

      And Gary. Sigh. "None of the papers presented a modeling method for experimenting with the cognitive mechanisms" of salmon is not a valid criticism of what was presented. If as you state "Darwinian theory" gives "easy answers" to questions like why salmon migrate, isn't it possible that those are also the correct answers? Sigh.

      Delete
    17. bwilson295 believes: In unguided evolution, genes of individuals who leave more offspring become more frequent in the populations. Animals within a species vary in how much care they give their offspring. In some cases, giving more care results in more offspring surviving and reproducing. In those cases, genes related to caring for offspring will increase in the population. In following generations, parents still vary in how much care they give and the process is repeated. Parental care can evolve in unguided evolution.

      Reproductive success is greatly increased by reproducing more than once per lifetime. You did not rule out the possibility that they are simply cognitively guided towards doing things the hard way, because of that being part of their millions of years old learned behavioral knowledge.

      If you believe that you just described "unguided evolution" then you now need to describe what "guided evolution" looks like. And invoking an untestable religious deity is not scientifically acceptable. I require a scientifically testable answer.

      Delete
    18. And bwilson stop helping N.Wells move the goalposts. The questions now under discussion are:
      How do we prove the guided evolution? Where do we start?

      On the other hand, how do we prove that guided evolution didn't happen?


      I need to see what your "guided evolution" looks like.

      Delete
    19. And the same goes for you judmarc. Show me what your "guided evolution" and "unguided evolution" looks like.

      Delete
    20. Unguided evolution is what over 150 years of research in numerous scientific disciplines supports and reaffirms. Guided evolution is a completely unevidenced fairy tale.

      If you think life would "go off the rails" without something to guide evolution, you don't know enough about evolution. I'm continually surprised by the people commenting on this blog and others who think their ignorance of the facts constitutes a challenge to said facts, rather than a challenge to them to rid themselves of their ignorance.

      Delete
    21. That is not a scientific answer judmarc. Sorry.

      Delete
    22. How about this: in guided evolution, mutations arise preferentially when they are needed, and of the sort to increase fitness. In unguided evolution, mutations are random with respect to their fitness effects. All we need now is for someone to to an experiment to determine which applies. Or perhaps someone already has done that experiment? Somebody with a name like "Lederhosen"; no, that isn't quite it.

      Delete
    23. GG wrote, "I need to see what your "guided evolution" looks like." Guided evolution is not my hypothesis. It's not my job to say what predictions it makes. The people who think guided evolution happens should not only make the predictions, but also WANT to make them so that we advocates of unguided evolution don't make the wrong predictions.

      Of course, some people have made relevant predictions, as John Harshman points out. Tests have been made. And how did that turn out? Perhaps you have some newer, better predictions that can be tested?

      Delete
    24. That is not a scientific answer judmarc

      "[W]hat over 150 years of research in numerous scientific disciplines supports and reaffirms" is not a scientific answer? Suppose you tell me what *is* scientific, *other than* what the research and scientific evidence supports?

      Delete
    25. In fact a fellow named Barry Hall published a very informative series of papers on so-called "directed evolution." In the initial papers he thought E. coli were not only accelerating mutations under stress but accelerating favorable ones. After doing additional experiments he backed off that initial thinking. It turned out the mutations that occurred most often were those that one would expect just on the basis of math (those involving the fewest non-fatal changes in bases).

      Or to put it even more simply, if evolution were guided, Lenski's long term evolution experiment wouldn't have had to be long term, would it?

      Delete
    26. Eric,

      "Well, the problem is obvious, because neither humans nor bananas look not even close to 50% of their 50% identical DNA. "

      What do you mean by "50% identical DNA"? Identical in nucleotide sequence, or what? Can you provide a peer-reviewed scientific paper that presents the data to support the 50% conclusion?

      "All I want to know, with the scientific knowledge that Darwinists claim to have, how to tweak the banana genes to make it look like a human which, I'm sure "the big science" will deny by adding billions of years of random, blind processes that figured it out how a banana became mobile with legs and then it spoke...

      This is nonsense. "

      Yes, that is nonsense. Evolution claims nothing of the sort. Sounds more like a creation myth.

      Delete
    27. PZ Myers has a "crocoduck" tie for this sort of nonsense.

      And Eric, I've got your bananaman (or in this case, bananawoman) picture for you, just so you won't be disappointed:

      http://www.tvacres.com/admascots_misschiquita.htm

      Delete
    28. bwilson says: Of course, some people have made relevant predictions, as John Harshman points out.

      For a recap of some of the relevant predictions made by the model I developed:

      "Guided evolution"
      The combined knowledge and behavior of all three intelligence levels guides spawning salmon of both sexes on long perilous migrations to where they were born and may choose to stay to defend their nests "till death do they part" from not being able to survive for long in freshwater conditions. Motherly alligators and crocodiles gently carry their well guarded hatchlings to the water, and their fathers will learn to not eat the food she gathers for them. If the babies are scared then they will call and she will be quick to come to their aid and let them ride on her head and body, as they learn what they need to know to succeed in life. For humans this instinctual and learned knowledge has through time guided us towards marriage ceremonies to ask for "blessing" from a conscious part of us that our multicellular intelligence level (brain) may be able to sense coming from the other intelligence levels we cannot directly experience, which at the genetic intelligence level has for billions of years been alive, and is now still alive inside of us.

      "Unguided evolution"
      Salmon would squirt out their eggs in the ocean then let the other fish eat them. Alligators and crocodiles would eat their young. Humans would be "meat robots" that have no need for marriage ceremonies and discard their young soon after birth.

      I am not interested in talking about what others have said, or entertain religious answers.

      If you cannot find a problem with the testable model and theory I have then I won. "Guided evolution" is scientifically accounted for by the above.

      Delete
    29. It's interesting to hear that evolution can be "guided" simply by having natural selection that favors genetic variants in salmon that have them bury their eggs instead of squirting them randomly around.

      It is interesting to hear that evolution can be "guided" by random mutational variation being selected, without some external guidance. i.e. it's interesting to hear that guided doesn't mean guided.

      Delete
    30. Joe, the source of the guiding (not natural selection) intelligence was an unknown. And theologically speaking the source has to at least in part be internal for meditative prayers to have any influence, on anything.

      From my experience it's primarily the anti-religious crowd that conceptualized an external Santa Claus type "intelligent designer", not serious theologians.

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

    ReplyDelete