Thursday, April 30, 2015

Nessa Carey doesn't understand junk DNA

Nessa Carey is a science writer with a Ph.D. in virology and she is a former Senior Lecturer in Molecular Biology at Imperial College, London.

She has written a book on junk DNA but it's not available yet (in Canada). Judging by her background, she should be able to sort through the controversy and make a valuable contribution to informing the public but, as we've already noted Nessa Carey and New Scientist don't understand the junk DNA debate.

Casey Luskin has a copy of the book so he wrote a blog post on Evolution News & Views. He's thrilled to find someone else who dismisses junk DNA and "confirms" the predictions of Intelligent Design Creationism. I hope Nessa Carey is happy that the IDiots are pleased with her book [New Book on "Junk DNA" Surveys the Functions of Non-Coding DNA].

I placed an order for the book and noticed that you can browse the first few pages.

How bad is it? ... Really bad. She starts out explaining what she means by "junk" DNA.
There's a bit of linguistic difficulty in writing a book on junk DNA, because it is a constantly shifting term. This is partly because new data change our perception all the time. Consequently, as soon as a piece of junk DNA is shown to have a function, some scientists will say (logically enough) that it's not junk. But that approach runs the risk of losing perspective on how radically our understanding of the genome has changed in recent years.

Rather than spend time trying to knit a sweater with this ball of fog, I have adopted the most hard-line approach. Anything that doesn't code for protein will be described as junk, as it originally was in the old days (second half of the twentieth century). Purists will scream, and that's OK. Ask three different scientists what they mean by the term 'junk', and we would probably get four different answers. So there's merit in starting with something straightforward.
There are so many errors crammed into these two paragraphs that it would take another book to correct them. Let me just point out that knowledgeable scientists define junk DNA as DNA that doesn't have a function. No other definition is worth the paper it's written on.

There was never a time when knowledgeable scientists said that all noncoding DNA was junk. Not in the last century, and certainly not in this century. Nessa Carey is not speaking the truth here. I don't think she's lying—although I don't rule out that possibility—but I do think she is seriously mistaken. How in the world could she write a book on junk DNA without learning how the term is defined?

I also don't think it's correct to say that our understanding of the genome has changed radically in recent years. Mine certainly hasn't and I'm pretty sure that most knowledgeable scientists had a good understanding of genomes 30 years ago. The only exception might be that there are more genes making functional RNAs than we realized back in the 1980s.

On the other hand, the views of some other scientists have changed a lot. They have learned, to their surprise, that most of our genome is junk and that natural selection has not eliminated all nonfunctional DNA. I don't think that's what Nessa Carey is referring to.

The debate over junk DNA is not about the existence of junk—that fact cannot be contested. The debate is over the relative amount of junk DNA in various genomes. There's plenty of real, positive, evidence that the human genome has lots of junk DNA (non-functional DNA) but there are still legitimate scientific discussions about the details and there are even debates about possible structural roles for nonconserved DNA (bulk DNA hypotheses). If a journalist is going to write about this stuff, they have to do a lot of homework. This is no place for amateurs.
For years scientists had no explanation for why so much of our DNA doesn't code for proteins. These non-coding parts were dismissed with the term 'junk DNA'.
Nassa Carey should read Five Things You Should Know if You Want to Participate in the Junk DNA Debate. Back in the 1970s, scientists had two kinds of explanations for noncoding DNA. The first explanation was that some of it was known to be functional. Scientists knew about regulatory sequences, origins of replication, centromeres, telomeres, and various genes for RNA. Later on we learned about introns.

The second explanation was that a lot of the DNA in eukaryotic genomes didn't have a function. Much of the human genome, for example, consisted of repetitive sequences that seemed to be dispensable. We knew that only a small percentage of the genome could be functional because of genetic load arguments. By the 1980s we knew about pseudogenes and we knew that most of the transposons in the human genome were defective bits and pieces. It was easy to explain this as junk because it certainly looked like junk.
But gradually this position has begun to look less tenable, for a whole host of reasons.

Perhaps the most fundamental reason for this shift in emphasis is the sheer volume of junk DNA that our cells contain. One of the biggest shocks when the human genome sequence was completed in 2001 was the discovery that over 98 per cent of the DNA in a human cell is junk. It doesn't code for any proteins.
We had an accurate measure of the size of the human genome back in the 1960s. We knew back then that there were probably fewer than 30,000 genes and that only a small fraction of the genome was complementary to mRNA.

When the decision to sequence the human genome was being discussed in the late 1980s, there were many scientists who said that it would be a waste of money because so little of it coded for proteins. There were no surprises, among knowledgeable scientists, when the draft sequence was published. Most of the genome appeared to be junk, just as expected.

If you were surprised then it was only because you hadn't been keeping up with the literature.
The other shock from the sequencing of the human genome was the realisation that the extraordinary complexities of human anatomy, physiology, intelligence and behaviour cannot be explained by referring to the classical model of genes. In terms of numbers of genes that code for proteins, humans contain pretty much the same quantity (around 20,000) as simple microscopic worms. Even more remarkably, most of the genes in the worms have directly equivalent genes in humans.
Anything found to be true of E. coli must also be true of elephants.

-Jacques Monod (1954)
Knowledgeable scientists already knew that humans had about the same number of genes as other animals. Knowledgeable scientists read the papers on the molecular biology of development—mostly in Drosophia—that were published in the 1980s. They realized that the differences between fruit flies, nematodes, and mammals were due largely to small changes in regulatory sequences. That's what evo-devo was all about. The concept was developed over the preceding 50 years.

Apparently, that concept is foreign to Nessa Carey. One wonders what sort of molecular biology she taught to students at Imperial College.

Knowledgeable scientists were not "shocked" to learn that humans had about the same number of genes as other animals and that all animals had similar genes. Stupid scientists might have been shocked but you don't write books about the misconceptions of stupid scientists—unless you are one.
As researchers deepened their analysis of what differentiates humans from other organisms at the DNA level, it became apparent that genes could not provide the explanation.
Genes plus regulatory sequences provide the explanation. That was known 40 years ago and it's still true today.
In fact, only one genetic factor generally scaled with complexity. The only genomic features that increased in number as animals became more complicated were the regions of junk DNA. The more sophisticated an organism, the higher the percentage of junk DNA it contains. Only now are scientists really exploring the controversial idea that junk DNA may old the key to evolutionary complexity.
I'm not making this up. A science writer with a Ph.D. actually wrote this in a book published in 2015!
... those ignorant of history are not condemned to repeat it; they are merely destined to be confused.

Stephen Jay Gould
Ontogeny and Phylogeny (1977)
Researchers are only just beginning to unravel the subtleties and interconnections in the vast networks of junk DNA. The field is controversial. At one extreme we have scientists claiming experimental proof is lacking to support sometimes sweeping claims. At the other are those who feel that there is a whole generation of scientists unable to see or understand the new world order.
I'm in the second category. There's a whole generation of scientists who seem to be completely ignorant of the history of their field so they make up stories that are out of touch with reality. They don't understand the major conceptual advances of the second half of the 20th century, especially evolution (population genetics), the molecular biology of development, and genomics.

They don't see or understand the new world order because they, and their teachers, missed the revolution that took place 30 years ago. It will take them a few more years to realize that most of our genome is, indeed, junk and that this is supported by lots of evidence. Eventually they will realize that a genome full of junk is compatible with evolution. Meanwhile we will probably have to put up with more nonsense like the nonsense in this new book.


76 comments :

  1. "I hope Nessa Carey is happy that the Idiots are pleased with her book"

    Priceless.

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    Replies
    1. I hope she's not and recalls the book

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    2. Maybe I'm reading you wrong here? Should a scientist suppress thoughts that might please ID/creationists? I've only heard one man honest enough to say his atheism comes before his science, it was Atkins I believe. Do you feel this way professor Moran?

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    3. Should a scientist suppress thoughts that might please ID/creationists?

      Definitely not.

      However, if you discover that creationists are excited about your ideas then chances are high that you are wrong.

      Delete
  2. "Rather than spend time trying to knit a sweater with this ball of fog, I have adopted the most hard-line approach. Anything that doesn't code for protein will be described as junk, as it originally was in the old days (second half of the twentieth century)."

    *faceplanet*

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    Replies
    1. Unbelievably stupid paragraph.

      How did the editor let that through?

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    2. Sort of feels like this...

      http://xkcd.com/1519/

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    3. Sometimes I have self-doubts about my general competency in regards to a future career involved with science.

      Then I see that books like these get published and sigh in relief.

      Delete
  3. "In fact, only one genetic factor generally scaled with complexity. The only genomic features that increased in number as animals became more complicated were the regions of junk DNA. The more sophisticated an organism, the higher the percentage of junk DNA it contains. Only now are scientists really exploring the controversial idea that junk DNA may old the key to evolutionary complexity."

    Looks like she might have been reading John Mattick.

    ReplyDelete
    Replies
    1. She believed Mattick's infamous Dog's Ass Plot.

      Forms this moron think the African lungfish is 50x more complex than humans?

      No. She has just never heard of the African lungfish... or the Niuse river water dog... or Polychaos dubium...

      But surely, even this moron must have heard of Christmas trees and their vast genomes full of "junk"?

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    2. From Nystedt et al (2013), The Norway spruce genome sequence and conifer genome evolution, Nature 497 (7451):

      "Conifers have dominated forests for more than 200 million years and are of huge ecological and economic importance. Here we present the draft assembly of the 20-gigabase genome of Norway spruce (Picea abies), the first available for any gymnosperm. The number of well-supported genes (28,354) is similar to the >100 times smaller genome of Arabidopsis thaliana, and there is no evidence of a recent whole-genome duplication in the gymnosperm lineage. Instead, the large genome size seems to result from the slow and steady accumulation of a diverse set of long-terminal repeat transposable elements, possibly owing to the lack of an efficient elimination mechanism."

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    3. That reference give me hope. I recently sat through a seminar that discussed large genome size variation in a plant genus. Throughout the seminar they referred to the small-genome plant as the "primative" form with "higher" variants having larger genomes that "must be adaptive". They never backed this assertion with any sort of molecular tree...

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    4. They never backed this assertion with any sort of molecular tree...

      But the most the tree would tell them is the order of events, not whether the later event was adaptive.

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    5. Exactly. They already "knew" the answer because bigger=more complex. No need to check it. An unbiased tree might have messed with their assertion ;-)

      THEN the "must be adaptive" layer on top of that.

      Delete
  4. Carey wrote, "The more sophisticated an organism, the higher the percentage of junk DNA it contains."

    Does "more sophisticated = more junk DNA" work both ways? Are onions therefore more sophisticated than humans? (They certainly have a more elegant shape.) And are some onions much more sophisticated than others? (They vary in the amount of apparently junk DNA they have.)

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    Replies
    1. I have no problem with the notion that onions are more sophisticated than humans... At a biochemical level.

      Where C value paradox becomes problematic is when certain lineages of onions have significantly more or less DNA then other lineages of onions

      That only means that the nondescript function bulk DNA acting as clean-fill (as suggested by Doolittle) could be possessed of some fudge factor

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    2. "The more sophisticated an organism, the higher the percentage of junk DNA it contains."

      Correlation and causation ... Sophisticated organisms tend to be bigger and have smaller populations, ergo selection against is weaker. Sophisticated organisms tend to invest heavily in large feeding somas which more than pay for themselves, earning a surplus in the energy and materials budget which reduces the selective cost of extra base pairs in their cells.

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    3. But how does one measure sophistication? Does sophistication equal size?

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    4. Piotr, shall we ask the humble Amoeba dubia?

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    5. Dammit, any newt has more junk DNA than a whale, let alone a human. Bats have less than mice -- apparently there's nothing sophisticated about echolocation and flight ;)

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    6. But Piotr, whales were created as a kind, complete with vestigial hind limb bones to test our faith. Echolocation and flight are easy for god, so why would a bunch of junk DNA be needed? You just have to free your mind :)

      Delete
  5. "We knew that only a small percentage of the genome could be functional because of genetic load arguments."

    Really? What's the argument? Another theory that can't be verified and tested? Since genetic load argument is bs, most of the the genome could and probably is functional. But when Darwinists are trying to fit their theory (without any evidence) into their dogma, it is unfortunately very hard to accept the obvious...for them

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    1. genetic load argument is bs

      I.e., not understood by you. But there's no reason at all you shouldn't, it's really dead simple to realize why it must be true. I'd say then that the cause would have to be a wish not to understand on your part.

      Delete
    2. Yeah, only Darwinists have been given the privilege of understanding something that evidence indicates should be view with a grain of salt

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    3. Another theory that can't be verified and tested?

      Simply amazing...

      1) The size of the human genome was known with a reasonable level of precisions somewhere in the 1950s

      2) The genome was sequenced 15 years ago.

      3) Since then thousands of genomes have been sequenced

      4) The mutation rate has been measured in all sorts of ways starting decades before there was genome sequencing and continuing to the present

      The calculations are trivial once you know those things

      And were done back in the 1960s, when people were just starting to work out the molecular biology of gene expression, didn't really have a clue what a transposon was, and didn't even suspect introns existed,

      Everything we have found out since then supports the predictions made back then. Which is the hallmark of successful theory.

      5) Moreover, now so much mapping of human variation has been done, that exercises like the one in Figure 6 here:

      http://nar.oxfordjournals.org/content/39/16/7058.full.pdf

      can and have been done many times and always return what is shown there.

      So what exactly is "untested" and "unverified" here?

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    4. Are you referring to the genetic load theory Georgi?
      If yes, are you suggesting that if our genome wouldn't have say 90% of jDNA, the genetic load would be to high and we would have been extinct millions of years ago?

      Or, are you talking about something else?

      Delete
    5. @Pest

      If you don't have anything intelligent to say about genetic load then don't say anything at all. I'm getting tired of reading your inane comments and I'll delete anything that doesn't make a contribution to the discussion. Feel free to contribute as long as you have something worth reading..

      Delete
    6. Larry, I know you worship this BS. All I want is THE SCIENTIFIC AND EXPERIMENTAL EVIDENCE you obviously have for the issue. Just don't go dumb or delayed it for months like you usually do when you don't have NO answers. Please Larry.





      Delete
    7. Ok, Larry what's genetic load? You are the host and more. It, is your turn.

      Delete
    8. Pest you illiterate numskull, Georgi's post is RIGHT FUCKING THERE.

      Delete
    9. U Elk, you have been around long enough to know that Pest's 'strategery' is classic religious creationist. No matter what evidence is presented, if it creates cognitive dissonance with his/her chosen religious beliefs, (s)he will simply ignore it and ask again for the evidence. (s)he's used to pretending.

      Delete
    10. Those who are truly interested can Goggle "Sandwalk genetic load."

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    11. For those truly interested:

      From Larry’s neck of the woods:

      Mutation Load: The Fitness of Individuals in Populations
      Where Deleterious Alleles Are Abundant

      Aneil F. Agrawal1 and Michael C. Whitlock2
      Department of Ecology & Evolutionary Biology, University of Toronto, Toronto, Ontario,
      Canada M5S 3B2; email: a.agrawal@utoronto.ca Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
      V6T 1Z4; email: whitlock@zoology.ubc.ca

      Mutation Load: The Fitness of Individuals in Populations Where Deleterious Alleles Are Abundant

      Most important excerpts:

      “The average human carries 250 to 300 loss-of-function
      mutations (1000 Genomes Project Consortium 2010). Inferences from molecular population genetics data indicate that the average person also carries another several hundred less
      severely deleterious amino acid variants (Eyre-Walker et al. 2006, Charlesworth & Charlesworth
      2010). Based on the amount of sequence constraint across the genome (Eory et al. 2010), it is ¨
      reasonable to speculate that the number of deleterious alleles carried at noncoding sites at least
      matches, and is likely several times greater than, the number at nonsynonymous sites.
      It is thus reasonable to say that the average human carries well over a thousand deleterious mutations “- and not 90 like Larry claims.

      “HOW TO STUDY LOAD EMPIRICALLY
      Given that deleterious mutation rates in many multicellular organisms are on the order of U = 1
      or more (Baer et al. 2007, Halligan & Keightley 2009, Keightley 2012), then there should be
      substantial mutation loads in these taxa. But are individuals really as much less fit as predicted
      by Haldane? If not, then why not? Despite the topic being of continued theoretical investigation
      for more than 70 years, there is very little evidence that Haldane’s theory is even approximately
      correct, even though the predicted effects should be large.
      The problem of identifying a mutant-free reference genotype makes measuring the absolute
      mutation load a near impossible task”


      I think this is enough for now. For those interested in reading the entire article, here is the link:

      Mutation Load: The Fitness of Individuals in Populations Where Deleterious Alleles Are Abundant

      Delete
    12. That paper (Agrawal and Whilock, 2012) discusses the actual value of the mutation load. The issue is whether populations can tolerate one (1) deleterious mutation per generation or perhaps more (e.g. 2). The authors conclude that diploid populations can survive with two deleterious mutations per generation.

      This is important in applying genetic load arguments to the presence of junk DNA. We know that humans have about 130 new mutations per generation and that approximately 10% of the mutations in functional DNA are likely to be deleterious.

      If all of our genome was functional then that would mean 13 deleterious mutations per generation. This is intolerable by all known criteria.

      However, if 90% of our genome is junk then there are only 13 mutations in functional DNA and only one or two of them are deleterious. This is in line with the paper you quoted. It means that most of our genome must be immune to mutation or we would not be here.

      The genetic load argument is a powerful argument for junk DNA.

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    13. The genetic load argument is a powerful argument for junk DNA.

      Pretty much the archetypal argument for junk DNA. http://twileshare.com/uploads/Ohno_1972.pdf

      Delete
    14. Pest, guess you didn't realize the 1000 and 250-300 figures you quote are measuring different things than the 90 Dr. Moran is talking about, eh?

      Delete
    15. It seems to me that the genetic load argument has an interesting consequence: it predicts the existence of an upper limit of the amount of functional DNA a diploid organism may have, depending on the mutation rate per base per generation. It seems this limit was reached early in the evolution of eukaryotes, so that, no matter what their phenotypic complexity, size, or position on the Dog's Arse Plot, they can be expected to have a similar amount of functional (coding, regulatory) DNA plus a variable amount of junk.

      Delete
    16. Larry,

      Isn't the foundation of your/and others assumption the key to the
      speculations you are trying squeeze in as science?

      Delete
    17. Pest, it was incredibly ignorant and rude for you to compare Larry's quoted 90 muatations-- which referred to new mutations in each new baby not in its parents-- against the paper's 1000 deleterious mutations, which was the total load accumulated over many generations.

      That's the difference between the interest on a loan, and the principal. It is a very serious error.

      You have not conceded you were wrong. That makes you look very dishonest.

      Now you seem to be trying to change the subject to new falsehoods, in an attempt to distract us. Gish gallop.

      Furthermore you asserted that the genetic load argument was not evidence, but "another theory that can't be verified and tested" and "BS" that Larry "worships", when you clearly have no clue what genetic load even means. It's trolling.

      I rarely call for creationists to be banned, as I enjoy humiliating them, but if you're going to lie in such an arrogant and rude way, I'll recommend that Larry bans you.

      I'm sure many here would vote with me. Pest needs to be taught a lesson.

      Delete
    18. I sometimes think that Pest is aiming for a banning. It must be frustrating for creationists, who have no evidence on their side and who have limited understanding of real science, to realize they cannot compete intellectually on a site like this. Faux martyrdom in the form of banishment is the closest that can be found to a shining path.

      Delete
    19. Pest's MO is never to make a scientific point, but just toss a word salad of creationist words, "theory (without any evidence)", "assumption", "speculation", "dogma", "theory that cannot be verified or tested", etc. in all contexts, in all situations, no matter that the evidence is jammed under his nose with references, he just keeps tossing the same word salad. If a lawyer tried that in a court of law, the judge would find him in contempt of court. It's ban-worthy.

      Delete
    20. It could be argued that the one positive thing Pest provides is prompting people to respond and explain a concept in extremely simple terms (as Larry did above) which is educational for lurkers, though evidently pointless to teach Pest anything.

      I'd hardly miss him if he's banned though.

      Delete
    21. It could be argued that the one positive thing Pest provides is prompting people to respond and explain a concept in extremely simple terms

      That's a good point. If Pest understood this, he would not be pleased.

      Delete
    22. That's why I read blogs like this. To see the explanations. I can scroll over the twaddle that inspires the explanations.

      Delete
    23. @Pest "It is thus reasonable to say that the average human carries well over a thousand deleterious mutations “- and not 90 like Larry claims."

      Your creationism is making you dumb. The ~90 mutations (actually more like 130, but w/e) are the number introduced every new generation. The "well over a thousand" in the piece you quote is the total amount being carried, not the amount being introduced in the next generation.

      Pest, it helps if you understand at least the basics first.

      Delete
  6. Nature had something of a review of three books on that topics yesterday, this one is among them.

    http://www.nature.com/nature/journal/v520/n7549/full/520615a.html

    Really frustrating to read

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  7. "Casey Luskin has a copy of the book so he wrote a blog post on Evolution News & Views. He's thrilled to find someone else who dismisses junk DNA and "confirms" the predictions of Intelligent Design Creationism."

    Why would Intelligent Design Creationism predict no junk DNA?

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    1. Because a genome full of junk doesn't look designed and because the creationist gods wouldn't make mistakes.

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    2. So, I guess the IDers have enough evidence to rule out the hypothesis that the designer was feeling especially artsy the day he/she/it created genomes and added some junk to them :P

      Delete
    3. In order to do this, the ID believer has to make assumptions about the designer for which there is no evidence, for example that the designer has some sort of aesthetic notion that junk DNA is just too messy or unseemly for its creation. How can they know that? Perhaps the designer doesn't care is there's some junk around.

      The presence or absence of junk DNA says absolutely nothing about the existence of a designer.

      Delete
    4. True. If ID proponents treated the ID hypothesis as science, they could not rule out Junk DNA, because the Great Omnipotent Designer could have created humans as vectors to carry around broken transposons. If ID were a scientific hypothesis, how could they rule that out?

      They only rule that out-- and assert 100% of our DNA is functional-- because they're smuggling in their religious assumptions about how they know the purposes and intents of the Great Omnipotent Designer with absolute certainty. That's their religious belief, it only comes from the Bible, and it never logically followed from the ID hypothesis.

      They know the purposes of the Great Omnipotent Designer with absolute certainty. They know he hates junk DNA and gay sex, he wants lower taxes on the rich and he won't allow global warming and pollution to #$%& our environment. They know this about GOD, but those beliefs aren't science, they're religion and politics.

      Delete
  8. I have two questions for anyone who has might have picked up a copy of the book: is Carey's book based mostly around the human genome? And does she reference any of Mike Lynch's work? I suspect the answers are yes and no.

    ReplyDelete
  9. Hmmm.
    If suiting ID then maybe its advancing progress about concepts in evolutionary biology being wrong. If so these things will happen as time goes on.
    Somebody is wrong. If she is wrong then how can creationists be said to not be doing science or good science. Is she not a true scientist or a good one even if wrong?
    What are the competence rules in origin matters?
    How can a scientist be wrong? Where did the investigation fail?
    Its suggestive of a option that origin investigations are not really scientiofic ones but are really hunches and then a case made on sparse evidence. This because its not easily open to investigation. Its not like physics. Its more complicated and demands more intellectual attention.
    Anyways everytime I turn around there is some more criticism of something about evolution presumptions.
    YEC and ID were here first and deserve to divide up the carcass.

    ReplyDelete
    Replies
    1. "YEC and ID were here first and deserve to divide up the carcass."

      In science, the ideas to get there first usually turn out to be wrong. Science continually revises itself in light of new data to better explain the natural world. That's why ID/YEC aren't science. They believe they already have the answers, and interpret everything through that lens of dogma. ID/YEC is a science stopper.

      Delete
  10. Nobody WANTS to read the bold text. That's not in English for obvious reason:

    The problem of identifying a mutant-free reference genotype makes measuring the absolute mutation load a near impossible task"
    It seems nothing is impossible for Darwinian faith.

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    Replies
    1. The very next word is HOWEVER.

      HOWEVER.

      "However, major tenets of mutation load theory should be
      testable by comparing individuals from populations that have evolved under different mutation
      rates. In a number of systems, mutation rate can be manipulated in replicate populations."

      What lies you got this time?

      Delete
    2. However, if you're a Darwinist, anything is possible despite the evidence pointing the other way. The "evolution" miracle" has given a lot of otherwise unemployed peoples hope for income not the truth they would have resented if it meant otherwise no bread on their family table.

      Delete
  11. Yeah, ban Wikipedia.

    Genetic Load "Problems

    "One problem with calculating genetic load is that in order to do so you have to a have a “perfect” or “optimal” genotype with which to compare the population to; this kind of genotype simply does not exist. This is problem because it means that it is harder for scientists to gauge with accuracy how much load a population has, and how much load it can bear without being in danger. This means that all perceptions of genetic load should be taken with a grain of salt.[19]"

    The [19] reference is to the same article I referred to.

    I think Wikipedia will be banned on this blog for sure

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    Replies
    1. Ok, so Dr. Moran explained all of your "objections" to the genetic load argument, and in the posts that followed, several poster re-explained it all to you and how you were utterly wrong. Your last feeble twitch amounts to:

      without a description of a "perfect" or "optimal" genotype, we can't know how much mutational load a genome can withstand, so it all must be taken with a "grain of salt". The argument from ignorance, a creationist favorite. When you have had your ass handed to you, your next step is to throw doubt on some aspect of the argument which superficially looks critical. This works well in building arguments with people who don't know much about the science, or the credulous looking for a reason to dismiss hard data. But this is not a creationist forum.

      Ideas have consequences, and the unknown is not where scientists throw up their hands and declare things "mysterious and impossible to know". It is where we come to work every day. So if the references you cite provide you with a counter argument to the mutational load hypothesis, make your case.

      What are the consequences of an 'optimal' genotype? What impact would this have on the number of mutations a genome could withstand under an assumption of no junk DNA, versus an assumption of some amount of junk DNA? Tell us the implications of your reference [19] on the junk DNA discussion.

      Delete
    2. @Pest "This is problem because it means that it is harder for scientists to gauge with accuracy how much load a population has, and how much load it can bear without being in danger."

      The key word there is 'harder', Pest. It makes it difficult, not impossible. Try heading with comprehension next time, instead of just scanning the text for areas of uncertainty and then trying to dismiss the whole thing because something is only known to an approximation.

      Delete
    3. Pest's quote mining amply demonstrates his lack of understanding to any outside observer who would come to this blog, so please keep doing what you're doing, Pest. You show better than we ever could the difference between a doubt willfully manufactured from fear and ignorance, and a desire to learn.

      The last quote mine showed you didn't recognize the simple distinction between mutations *per generation* versus the *total number of mutations* present in an individual's genome (considering both inherited mutations and mutations per that individual's generation) versus the number of *deleterious mutations per generation* versus the *total number of deleterious mutations* present in an individual's genome (considering both those inherited and those that occurred in the individual).

      Your latest quote mine shows a similar elementary lack of reading comprehension. It simply says it would be great to know what a "perfect" genome is as a zero point from which to calculate a precise mutational load. It doesn't say mutational load isn't a problem; it doesn't say this problem wouldn't eventually result in extinction if the deleterious mutations were all in critically important DNA (which would be the situation if there were no junk).

      This is very much the same as saying it would be nice to know how much money you started with in an account that earns no interest, so you can calculate exactly how long it will be before fees and expenditures make you bankrupt. It doesn't mean spending money without taking any in isn't a problem, and it doesn't mean you won't eventually go bankrupt.

      So what you've quoted isn't relevant in the least to a discussion of whether the mutational load argument supports the presence of junk DNA. It does support it, just as surely as the fact that money goes out for expenditures or fees means you have to earn income and/or interest to avoid going bankrupt.

      Delete
  12. Chris B,
    "without a description of a "perfect" or "optimal" genotype, we can't know how much mutational load a genome can withstand, so it all must be taken with a "grain of salt".

    Description? What do you want? A Facebook picture?
    This is not really my statement but Wikipedia's. I just happen to agree.

    "The argument from ignorance, a creationist favorite. When you have had your ass handed to you, your next step is to throw doubt on some aspect of the argument which superficially looks critical. This works well in building arguments with people who don't know much about the science, or the credulous looking for a reason to dismiss hard data. But this is not a creationist forum. "

    I prefer hard data over claims that Darwinist always supposed to have but they are nowhere to be found.

    Ideas have consequences, and the unknown is not where scientists throw up their hands and declare things "mysterious and impossible to know". It is where we come to work every day. So if the references you cite provide you with a counter argument to the mutational load hypothesis, make your case.

    What are the consequences of an 'optimal' genotype? What impact would this have on the number of mutations a genome could withstand under an assumption of no junk DNA, versus an assumption of some amount of junk DNA? Tell us the implications of your reference [19] on the junk DNA discussion."


    I don't know exactly what you are talking about above. If I tried to answer some of your questions, I would have turn science into religion. Because this is exactly what you are trying to defend.

    Reality check:

    The genetic load argument is built on an ASSUMPTION the human genome can't handle or would not have been able to handle the mutation load If ALL OR MOST OF HUMAN GENOME WERE "FUNCTIONAL"

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    1. "I don't know exactly what you are talking about above"

      This summarizes everything Pest reads on here.

      Delete
    2. "Description? What do you want? A Facebook picture?
      This is not really my statement but Wikipedia's. I just happen to agree."

      I didn't ask for a description here. That was a lame attempt at obfuscation, Pest. I reiterated your argument here, which amounted to selectively quoting bits of a Wikipedia page to build an argument from ignorance.

      "I prefer hard data over claims that Darwinist always supposed to have but they are nowhere to be found."

      You were given the hard evidence several times already in this thread. What you prefer is "evidence" to support your chosen religious dogma and mythological fantasies. We can't help you with that here.

      "I don't know exactly what you are talking about above. If I tried to answer some of your questions, I would have turn science into religion. Because this is exactly what you are trying to defend."

      The old 'science is religion' canard. And even after having mutational load explained to you several time in this thread? Have a little self respect and get some new material.

      "Reality check:

      The genetic load argument is built on an ASSUMPTION the human genome can't handle or would not have been able to handle the mutation load If ALL OR MOST OF HUMAN GENOME WERE "FUNCTIONAL""

      Actual reality check:

      The mutational load argument does not at all depend on "ALL OR MOST OF HUMAN GENOME WERE "FUNCTIONAL"". It doesn't assume any ratio of functional/junk DNA. Go back and read the posts in this thread explaining it to you in plain language.

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    3. Putz sez: The genetic load argument is built on an ASSUMPTION the human genome can't handle or would not have been able to handle the mutation load If ALL OR MOST OF HUMAN GENOME WERE "FUNCTIONAL""

      No, that is a conclusion, and an inevitable one, not an assumption. Pest either does not know what the word "assumption" means, or he knows and is deliberately trying to obfuscate the word "assumption." The latter is a common creationist strategy, deliberately using the word "assumption" to describe something that is not an assumption-- most often, a conclusion based on observations that is fatal to the creationist worldview. Every time we make a measurement or experiment with a conclusion that kills creationism dead, when we've really got them in a corner, they always scream "You ASSUMED that thing inconvenient for me!" Sure, Putz.

      The data shows that your DNA is 92-93% junk and cannot be more. That is a conclusion based on observations, and was never an assumption at any point in the history of science.

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  13. LOL, the whole scheme of organic evolution is build on assumptions and preconditions and conjections

    ...

    Evolutionism is a belief system that adheres to generatio spontanea ages after it was scientifically proven wrong.

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    1. This is demonstrably false. Christian-influenced creationism was the default, majority belief in Europe in Darwin's time. But there were problems with this theory, which were contradicted by the observations. (These problems still exist in your post-hoc rationalization attempts). This lead to a move towards a better explanatory theory. One that has been modified over time, but is still the best explanatory framework of the observations out there.

      I know to a believer like yourself, that is emotionally invested in your belief, the fact that we are not like you in our acceptance of evolution is hard to grasp. Right now, it is the best theory we have to explain the data. If a more compelling one comes along, it will win, and self-centered, career-driven folks like your idols at ENCODE will fall over themselves to become Darwin's replacement. But the stuff you are spouting is not that compelling.

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  14. The science dato of teh ENCODE are hard to swollow for the DArwinian science stoppers...

    Remeber Mendels laws, remember McClintock, remember ENCODE...

    The Darwinians are a disgrace to science.

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    1. http://judgestarling.tumblr.com/post/102457412896/do-long-noncoding-rnas-defy-evolutionary

      "Of course, the possibility exists that all the fundamentals of evolutionary biology are wrong, in which case you should do what Einstein did to Newton, replace one coherent theory that proved unsatisfactory by another coherent [theory]. Don’t just engage in special pleading and whine..."

      -Dan Graur (11/12/2014)

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  15. This comment has been removed by the author.

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    1. deleted, as this should have been posted as a reply, above...

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