Saturday, July 21, 2012

Ken Miller and Chromosome Fusion

[Ed: This post, from October 12, 2010, is worth a second look in light of Carl Zimmer’s recent piece on human chromosome fusion]

In the 2005 Kitzmiller v. Dover Area School District court case, federal judge John Jones was heavily influenced by the first expert witness, evolutionist Ken Miller. As Jones later recalled, he “was taken to school.” Unfortunately what Miller “taught” Jones was a series of scientific misrepresentations. Miller focused on two examples from molecular biology: a pseudogene and a fused chromosome. In both cases Miller gave Jones many facts but the lessons were carefully tailored to misrepresent both the science and evolutionary theory.

As I explained here, Miller’s pseudogene example included four key misrepresentations: that the pseudogene has no function and is broken, that the pseudogene DNA sequence has “errors” or “mistakes,” that there is no reason for broken genes aside from common descent, and that the evolutionary interpretation of such pseudogenes is objective science.

As was well known and documented when Miller and the ACLU lawyers devised Miller’s testimony, pseudogenes that had been investigated often exhibited functional roles, such as gene expression, gene regulation and generation of genetic diversity. Pseudogenes were found to be involved in gene conversion or recombination with functional genes. Pseudogenes sequences were found to be conserved with reduced nucleotide variability, excess synonymous over nonsynonymous nucleotide polymorphism, and other features that are expected in genes that have functional roles.

Any expert witness testifying on such a narrow topic would have been well aware of these well known results which were published by leading researchers in top tier scientific journals. And yet Miller gave no such perspective to the Dover court, and instead unequivocally represented his pseudogene example as non functional and broken. That was the evolutionary interpretation of pseudogenes, not what the scientific evidence was indicating.

And even if Miller’s selected pseudogene was truly broken, that would not mandate an evolutionary explanation as Miller unequivocally stated to the court. Miller told judge Jones that a pseudogene found in different cousin species, with common mutations, “must mean that these two organisms are descended with modification from another organism” and “leads us to just one conclusion,” which is evolution’s common descent. But this too was a lie, as any expert witness on this topic would know of the many instances of pseudogenes with mutations common to multiple species that do not fit the evolutionary pattern. In these cases even evolutionists must admit that common descent does not explain the mutations.

Perhaps most importantly, Miller’s pseudogene testimony misrepresented the evolutionary argument as objective science whereas Miller and the evolutionists, when not in federal court, make one religious argument after another. The religious foundation of evolution goes back to 18th century Enlightenment and before, and would automatically expel evolution from our public schools.

Miller’s pseudogene argument was just another example of a centuries-long history of religious mandates for evolution. Miller had been making such religious arguments for many years before Dover. He argued that life revealed features “that no engineer would stand for” so they must have evolved. That may be true, but such knowledge cannot come from objective science.

As Miller informed the Dover court, his pseudogene example was “just a mess.” That’s one of his favorite ways of making evolution’s religious argument. As he wrote more than 10 years before Kitzmiller:

In short, this sixth gene [the same pseudogene Miller testified of in the Dover court] is a mess, a nonfunctional stretch of useless DNA. From a design point of view, pseudogenes are indeed mistakes. So why are they there? Intelligent design cannot explain the presence of a nonfunctional pseudogene, unless it is willing to allow that the designer made serious errors, wasting millions of bases of DNA on a blueprint full of junk and scribbles.

It is a powerful argument, but it is not scientific. Miller routinely makes these religious arguments in his books and presentations, but they were carefully edited out for his testimony to the Dover court.

The ACLU lawyers and evolutionists argued that Intelligent Design is a religious theory because there was religious intent. They carefully traced this in early documents. But in evolutionary theory no such careful tracing is needed. The religious claims are boldly pronounced by evolutionists all through their literature. Darwin’s book was chocked full of religious claims, and today’s evolutionists are no different.

This hypocrisy of evolutionary thinking was equally evident in the second of the two examples Miller presented to the Dover court. In that example, Miller showed evidence that two of our chromosomes have been fused together and claimed it was powerful evidence for evolution: “the closer that we can get to looking at the details of the human genome, the more powerful the evidence has become.”

But from a scientific perspective, the fusion event occurred in, and spread through, the human population. There is no evolutionary relationship revealed. Even if evolution is true, this fusion event would give us no evidence for it. The fused chromosome did not arise from another species, it was not inherited from a human-chimp common ancestor, or any other purported common ancestor.

The reason why evolutionists find this argument to be so powerful is, once again, from a religious perspective. According to evolutionists, the evidence mandates evolution because it disproves creation and design. As evolutionist Barry Starr explains:

An alternative explanation is that the designers fused the two chromosomes together when they created humans. ...

The difficulty with this idea is that there is no obvious advantage to having 46 chromosomes instead of 48. ...

And even if there were, a designer who can easily put in the 60 million or so differences between humans and chimpanzees should be able to accomplish whatever results a chromosome fusion gives more elegantly than sticking two ape chromosomes together.

The power of the argument is not that evolution is confirmed, but rather than design is falsified. As Denis Alexander elaborates in his book Creation or Evolution, the fused chromosome “reveals our shared ancestry with the apes.” [211] Of course the chromosome reveals no such thing. It provides no more evidence for evolution than any other similarity. Starr, Alexander and the evolutionists may as well be discussing similarities we share with the apes in our bones or our biochemistry. But the evolutionists focus on cases such as the fused chromosome because these cases provide far more powerful religious evidence. As Alexander explains:

The suggestion that God has planted misleading ‘molecular fossils’ in our bodies is parallel to the suggestion that God planted misleading physical fossils in the rocks to test the faith of the believer. The obvious and profound theological problem with such a suggestion, as we considered in Chapter Six, is that it makes God into a deceiver on a grand scale. It would mean believing in a God who deliberately confuses people, making it look certain that we had shared common ancestry with the apes, when really this was not the case. [213]

And likewise Miller, when not deceiving federal judges, makes this same argument about the very evidence he presented in the Dover court:

So all we have to do is to look at our own genome, look at our own DNA, and see, do we have a chromosome that fits these features?

We do. It's human chromosome number 2, and the evidence is unmistakable. We have two centromeres, we have telomere DNA near the center, and the genes even line up corresponding to primate chromosome numbers 12 and 13.

Is there any way that intelligent design or special creation could explain why we have a chromosome like this? The only way that I can think of is if you're willing to say that the intelligent designer rigged chromosome number 2 to fool us into thinking that we had evolved. The closer we look at our own DNA, the more detailed a glimpse we get of our own genome, the more powerful the evidence becomes for our common ancestry with other species.

In his testimony, Miller told the Dover court that:

the closer that we can get to looking at the details of the human genome, the more powerful the evidence has become.

And when out of court, he makes the same statement:

The closer we look at our own DNA, the more detailed a glimpse we get of our own genome, the more powerful the evidence becomes for our common ancestry with other species.

The difference is he carefully omits the religion when in court. Nor did Miller reveal to the court that evolution is in no way required to explain the chromosome fusion evidence.

Miller also omitted several other inconvenient truths. Judge Jones said he received the equivalent of a degree in the expert testimony, but that degree didn’t include the fact that, beyond speculation, evolution has no explanation for how chromosomes evolved in the first place. And Miller did not explain the great number (more than a thousand) genes unique to the human genome. Again, beyond speculation evolution does not explain the rapid appearance of these novel genes. Indeed, as one evolutionist admitted, the secret to evolving a human from a chimp is to make fast changes in just the right places:

The way to evolve a human from a chimp-human ancestor is not to speed the ticking of the molecular clock as a whole. Rather the secret is to have rapid change occur in sites where those changes make an important difference in an organism’s functioning.

Finally, Miller presented the chromosome fusion evidence as a “beautiful” confirmation of an evolutionary prediction. What he didn’t explain to the court is that science is full of theories known to be false which yet make all kinds of confirmed predictions.

The Kitzmiller trial was one long series of misrepresentations. Yes judge Jones was schooled, but he didn’t learn the truth.

102 comments:

  1. Cornelius Hunter: "Nor did Miller reveal to the court that evolution is in no way required to explain the chromosome fusion evidence."

    What is the ID explanation for the chromosome fusion evidence? Coincidence? Asking seriously.

    ReplyDelete
    Replies
    1. Derick:

      Not sure, I suspect ID would take a scientific view, in contrast to evolution's dogmatic religious view. For instance, a fusion event could have caused it, but the scientific questions with that hypothesis (sequence at the proposed fusion site is not close to what you'd expect; the 48 chromosome population would have had to have gone extinct, etc) means a scientist needs to be cautious.

      Delete
    2. Excellent response. Indeed, why did the 48 chromosome population disappear from the face of the earth? This is puzzling when you consider that they were not just a simple majority since every human minus 1 (the one with the fusion event) had 48 ape chromosomes. What possible evolutionary advantage could the fusion event have given that first chromosome-challenged human?

      Evolution fails again. Hard.

      Delete
    3. CH: Not sure, I suspect ID would take a scientific view, in contrast to evolution's dogmatic religious view.

      O rly?

      Well, I'm glad to hear it, although as always I reject your absurd characterisation of the view you reject.

      For instance, a fusion event could have caused it,

      Right. In which case, chimps and humans would have common ancestry, right? As is indicated by a vast body of independent evidence.

      but the scientific questions with that hypothesis (sequence at the proposed fusion site is not close to what you'd expect;

      And what would you expect, Cornelius?

      I'm all ears.

      the 48 chromosome population would have had to have gone extinct, etc)

      What? What about the chimps? They aren't extinct!

      means a scientist needs to be cautious.

      Well, come on, then, Cornelius. Explain your scientific position here. I'm calling your bluff.

      Delete
    4. EL:

      What? What about the chimps? They aren't extinct!

      Your google searches still aren't working very well.

      Delete
    5. Explain, please, Cornelius.

      I asked you two questions. What are your answers?

      Or will you ignore them like all the other questions you have ignored so far?

      Delete
    6. Let me rephrase them for clarity:

      1. What sequence at the proposed fusion sitewould you expect?

      2. What do you mean by "the 48 chromosome population would have had to have gone extinct"?

      Delete
    7. Derick: What is the ID explanation for the chromosome fusion evidence? Coincidence? Asking seriously.

      Jeff: Separate ancestry. See http://www.uncommondescent.com/intelligent-design/why-the-chromosomal-fusion-argument-doesnt-wash/ for example.

      ID-style SA doesn't have to explain all the convergence posited by the CA approach. It doesn't have to account for the rates and kinds of evolution (i.e., the existence of the transitional species at the relevant times). IOW, all those posited CA events that are not predicted by any predictive model are mere hypotheses void of evidence, at this time.

      Delete
    8. Here is a prediction that I hope will be falsified:

      Cornelius will not answer my two questions.

      Delete
    9. Hunter:

      the 48 chromosome population would have had to have gone extinct, etc)

      Liddle:

      What? What about the chimps? They aren't extinct!

      This is pathetic. If I were Hunter, I would not reply to your questions either. We're not talking about chimps here. We're talking about the humans who supposedly descended from the common ancestor of both chimps and humans. Those humans had 48 chromosomes just like the chimps and the gorillas. Where are those chromosome-challenged humans? Why did they disappear? Evolution has no answer because being chromosome-challenged does not give a species a powerful evolutionary advantage. And also, the apes as proof that having 48 chromosomes is not a disadvantage.

      Liddle, your are either truth-challenged or IQ-challenged. What gives?

      Delete
    10. Liz, he gave a concise, albeit cryptic, answer:

      Your google searches still aren't working very well.

      I suppose we will have to work with this until such time that he willeth to speak again.

      Thoughts?

      Delete
    11. It's perfectly true that my google searches arne't working very well, except that I have now read the whole of Carl Zimmer's piece (for some reason the bottom of it hadn't loaded when I first read it) and I note that my first question is exactly the same as his.

      The Discovery Institute seem to want us to believe that there is some violation of prediction about the fused chromosome but they will not say what it is. All they will produce is cryptic clues.

      Bizarre.

      My second question I guess reflects the assumption (which may be true, I don't know) that the chromosome fusion happened after the chimpanzee lineage split, rather than being the cause of it, and I guess could be rephrased as: why did the fused chromosome go to fixation in that lineage?

      And one possibility is that a sub-population with the fused chromosome speciated, and the remainder continued for a while, then went extinct. Alternatively, there was linkage with a good set of alleles on the fused chromosome (or at least on the first individual who carried it), and that helped carry it to fixation. Or it was just drift.

      Not a problem anyway.

      But I'd still like to see Cornelius's attempt to answer:

      What sequence at the proposed fusion site would you expect?

      I'm calling his bluff. And Casey Luskin's.

      Delete
    12. Correction:

      I wrote above:

      Where are those chromosome-challenged humans?

      I meant to write:

      Where are those 48-chromosome humans?

      Delete
    13. Louis: This is pathetic. If I were Hunter, I would not reply to your questions either. We're not talking about chimps here.

      Well, yes, we are. Chimps and humans, and the evidence that the human Chromosome 2 is a fusion of Chimp chromosome 2 and 3, or something very like it, suggesting that chimps and humans diverged relatively recently, the human lineage carrying a fused version of the two original chromosomes, which remained unfused in the chimp lineage (hence 48 for them, and 46 for us).

      We're talking about the humans who supposedly descended from the common ancestor of both chimps and humans. Those humans had 48 chromosomes just like the chimps and the gorillas.

      How do you know? It's possible that the fusion happened a substantial while after the divergence, and that a second divergence occurred, one with the 48 chromosomes, and one with the 46, the first going extinct. But possible not - the fused chromosome could simply have gone to fixation within the one lineage.

      Where are those chromosome-challenged humans? Why did they disappear?

      They weren't "chromosome-challenged" exactly - having a fused chromosome isn't disastrous, and in fact, quite a few of us have them, and pass them to our offspring. Many variants go to fixation for no reason at all, apart from drift.

      Evolution has no answer because being chromosome-challenged does not give a species a powerful evolutionary advantage.

      And not all evolution is due to selection, powerful or otherwise. Sometimes it is a result of neutral drift. And there are also effects of linkage. If the first individual to have the fused chromosome was a particularly sexually active individual, and left a lot of offspring despite slightly reduced viable offspring per conception, then the viable offspring would inherit a lot of good genes along with the fused chromosome, and pass these along (together with their own inherited fused chromosome).

      And also, the apes as proof that having 48 chromosomes is not a disadvantage.

      No reason to think it would be.

      Liddle, your are either truth-challenged or IQ-challenged. What gives?

      You've excluded a middle, there, Louis. I'll leave you to work it out.

      Delete
    14. I wrote above:

      Where are those chromosome-challenged humans?

      I meant to write:

      Where are those 48-chromosome humans?


      Dead.

      Delete
    15. Me:

      We're talking about the humans who supposedly descended from the common ancestor of both chimps and humans. Those humans had 48 chromosomes just like the chimps and the gorillas.

      Liddle:

      How do you know? It's possible that the fusion happened a substantial while after the divergence, and that a second divergence occurred, one with the 48 chromosomes, and one with the 46, the first going extinct. But possible not - the fused chromosome could simply have gone to fixation within the one lineage.

      As expected, the 'possibles' and the 'coulds' are liberally mixed into this pseudoscientific sauce.

      An entire species changed its chromosome count. Why? Because it could.

      The 46-chromosomers completely displaced the 48-chromosomers. Why? Because they could.

      The 46-chromosomers completely out-copulated the 48-chromosomers. Why? You got it. Because they could.

      Wow. The science in all this is intense. LOL.

      Delete
    16. Louis As expected, the 'possibles' and the 'coulds' are liberally mixed into this pseudoscientific sauce.

      An entire species changed its chromosome count. Why? Because it could.

      The 46-chromosomers completely displaced the 48-chromosomers. Why? Because they could.

      The 46-chromosomers completely out-copulated the 48-chromosomers. Why? You got it. Because they could.

      Wow. The science in all this is intense. LOL.


      The problem here, Louis, appears to be that you don't understand enough biology to make sense of what I'm saying.

      Let's take a simpler example. Let's say that you have a novel mutation. You almost certainly have a great many, but we will call this one L. For Louis.

      Nobody in the world has ever had this sequence before you. L does nothing, however, has no effect on you at all.

      But you have several children, and half of them inherit L.

      They have children, and half of those inherit L.

      Many future generations go by. Your line flourishes, because you are a fine man, and you have good genes. Some of your descendents marry each other, and some of their children have LL (inheriting L from both parents).

      Now, L does nothing - is neither harmful nor beneficial. What happens to it? Well, there is a sporting chance, if the population is smallish, that it will die out completely. there is also a sporting chance that eventually everyone in the population will have two copies of L, especially, if, as I said, you are a fine figure of a man, and your descendents tend to be particularly virile.

      Let's say that the second thing happens - there comes a generation when everyone has two copies of LL. We say that L has "fixated" in the population

      We do not say that the non-L bearers have "gone extinct". They are no more "extinct" than the L bearers of the past, i.e. are merely dead. They have left lots of descendents in the population, it's just that all their descendents are also Louis's.

      It's not that the non-L bearers were out-copulated. They've been copulating just fine. It's just that they've been copulating with L bearers, and it's just turned out that their L bearing children have outnumbered the non-L bearing children.

      This is all standard population genetics.

      Now, substitute a fused chromosome for L. Add in the interesting factor that fused chromosome bearers whill be rather more fertile when mated with othe fused chromosome bearers than when mated with non-fused-chromosome bearers.

      This means that while initially, being a fused-chromosome bearer was slightly deleterious in itself (although may well have been compensated by the otherwise excellent genes borne by the original fused-chromosome bearer), as the fused-chromosome is propagated through the population, it it becomes less deleterious because the environment has changed, simply by virtue of their now being more fused-chromosome bearers, with whom mating is more fecund.

      Yet again you have dismissed the science without understanding it. Understand first, then criticise. Doing it the other way round makes you look a bit silly.

      Delete
  2. Replies
    1. No, but it can be uncomfortable.

      I recommend a regular high fiber diet.

      Delete
  3. And as with every thing else with Darwinism, the supposed evidence falls apart on scrutiny:

    New Research Undermines Fused Chromosome 2 Argument for Human Evolution - video
    http://www.youtube.com/watch?v=DyVVIfRNQOQ

    New Research Undermines Key Argument for Human Evolution by Jeffrey Tomkins, Ph.D. - February 2012
    Excerpt: 1. The purported fusion site on human chromosome 2 is actually located in a different position on chromosome 2 than predicted by the fusion model. The hypothetical fusion site is also in an area with suppressed recombination (meaning that the fusion sequence should be very pristine) and should exhibit very little degeneracy, compared to standard telomere sequence. Telomere sequences in humans normally consist of thousands of repeats of the standard 6-base sequence “TTAGGG.” We found that the hypothetical fusion region is completely degenerate and vaguely represents anything close to intact and fused telomeres. An earlier 2002 research report by molecular evolutionists also made note of this extreme sequence degeneracy and the obvious discrepancies it presented for the evolutionary model.3
    2. At the purported fusion site, there is a very small number of intact telomere sequences and very few of them are in tandem or in the proper reading frame. The small number of randomly interspersed telomere sequences, both forward (“TTAGGG”) and reverse (“CCCTAA”), that populate both sides of the purported fusion site are not indicative of what should be found if an end-to-end chromosomal fusion actually took place.
    3. The 798-base core sequence surrounding the fusion site is not unique to the purported fusion site, but found throughout the human genome with similar sequences (80 percent or greater identity) located on nearly every chromosome. This indicates that the fusion site is some type of commonly occurring fragment of DNA in the human genome.
    4. No positionally corresponding regions of sequence similarity in the chimpanzee genome for the purported human fusion site were found. The 798-base core fusion-site sequence did not align (match) to any corresponding regions in the chimp genome. In fact, the sequence was considerably less common and more dissimilar in chimpanzees.
    5. Queries against the chimpanzee genome with fragments of human DNA sequence (alphoid sequences) found at the purported cryptic centromere site on human chromosome 2 did not produce any significant hits using two different DNA matching algorithms (BLAT and BLASTN).
    6. The purported cryptic centromere on human chromosome 2, like the fusion site, is in a very different location to that predicted by a fusion event.
    7. The DNA alphoid sequences at the putative cryptic centromere site are very diverse and form three separate sub-groups. They also do not closely match known functional human centromeric alphoid elements. Alphoid sequences are commonly found throughout the human genome, and some types of alphoid sequences are not associated with centromeres. This strongly diminishes their probability of being part of an ancient de-activated (cryptic) centromere.
    http://www.icr.org/article/6089/

    ReplyDelete
    Replies
    1. Of somewhat related note, I liked this recent, very informative, video which refuted the ERV argument that is often used by Darwinists:

      (Refutation of) Endogenous Retroviruses (ERVs) argument - NephilimFree - July 2012 - video
      http://www.youtube.com/watch?v=TIz0UOfTVa8

      Delete
    2. NephilimFree!!!

      Honestly, ba77, if that's what you call a persuasive argument, then I will go back to not checking out your links.

      He just makes stuff up. Does the fact that he doesn't provide a single citation to back up his "facts" not ring any alarm bells with you?

      Here's a counter-video for you :)

      http://www.youtube.com/watch?v=4V-8HfEglHI

      Delete
    3. "He just makes stuff up."

      You mean he's really a Darwinist in disguise that 'just makes stuff up' just so to avoid falsification???

      actually I find his facts to line up with reality!

      a few cites:

      Endogenous retroviruses regulate periimplantation placental growth and differentiation
      http://www.pnas.org/content/103/39/14390.abstract

      Refutation Of Endogenous Retrovirus - ERVs - Richard Sternberg, PhD Evolutionary Biology - video
      http://www.metacafe.com/watch/4094119

      The Human Lineage Was Somehow “Purged” - Cornelius Hunter - April 2012
      Excerpt: Another such feature is the lack of endemic infectious retroviruses in humans. The problem is that these viruses are present in the other primates, and so according to evolutionists these viruses must be present in their common ancestor which, again according to evolution, would be an ancestor of humans as well.,, In other words, when evolution spontaneously created humans our DNA must have been “purged.” We got a do-over! Hilarious.
      http://darwins-god.blogspot.com/2012/04/unbelievableevolution-in-complete-free.html

      Retroviruses and Common Descent: And Why I Don’t Buy It - September 2011
      Excerpt: If it is the case, as has been suggested by some, that these HERVs are an integral part of the functional genome, then one might expect to discover species-specific commonality and discontinuity. And this is indeed the case.
      http://www.uncommondescent.com/evolution/retroviruses-and-common-descent-and-why-i-dont-buy-it/

      Endogenous Retroviruses (ERVS) A Case for Common Descent or A Case for Incorrect Presupposition?
      http://www.whoisyourcreator.com/endogenous_retroviruses.html

      Evolution or Creation - WHAT'S ERVs GOT TO DO WITH IT? - video
      http://www.youtube.com/watch?v=4zK81Zti9BM

      Related notes:

      Is "Pseudogene" a Misnomer?
      The term "pseudogene" may be as inappropriate as the term "junk DNA," according to the entry on pseudogenes in the 2010 Encyclopedia of Life Sciences, published by prestigious the academic publisher John Wiley & Sons,,
      http://www.evolutionnews.org/2011/01/is_pseudogene_a_misnomer042301.html

      Pseudogenes and the Origin of Humanity: A Response to the Venema Critique of the RTB Human Origins Model, Part 5 - Fazale Rana
      Excerpt: In his critique, Venema does acknowledge that research shows some pseudogenes are functional, but he dismisses this point by claiming that such pseudogenes are rare. This assertion, however, is not supported by the latest work. In fact, two of the articles on our website discuss papers (published in peer-reviewed journals) that emphasize how widespread pseudogene function actually is.
      Researchers have discovered that the genesis of certain classes of junk DNA is not rare and random, but occurs frequently and in a repeatable manner. (Go here and here to read recent articles.) Scientists have also learned that the order of genes along a chromosome plays a functional role as well.
      http://www.reasons.org/pseudogenes-and-origin-humanity-response-venema-critique-rtb-human-origins-model-part-5

      Delete
    4. as to backing up the fact that Darwinists are severely misleading (making stuff up) with 'fusion' evidence:

      Interstitial telomeric sequences (ITSs) are not located at the exact evolutionary breakpoints in primates. - 2009
      Abstract: Although their function has not yet been clearly elucidated, interstitial telomeric sequences (ITSs) have been cytogenetically associated with chromosomal reorganizations, fragile sites, and recombination hotspots. In this paper, we show that ITSs are not located at the exact evolutionary breakpoints of the inversions between human and chimpanzee and between human and rhesus macaque chromosomes. We proved that ITSs are not signs of repair in the breakpoints of the chromosome reorganizations analyzed. We found ITSs in the region (0.7-2.7 Mb) flanking one of the two breakpoints in all the inversions assessed. The presence of ITSs in those locations is not by chance. They are short (up to 7.83 repeats) and almost perfect (82.5-97.1% matches). The ITSs are conserved in the species compared, showing that they were present before the reorganizations occurred.
      http://www.ncbi.nlm.nih.gov/pubmed/19420924?dopt=Abstract

      Delete
    5. As well, Why did I cringe when you wrote the word "Honestly" before you issued a ad-hominem???

      Delete
    6. I have no idea, ba77.

      I was just amazed that you should cite NephilimFree as a credible source.

      Delete
    7. NephilimFree is far more credible than any neo-Darwinist will ever be in my book. For instance catch this blatant lie that Dawkins was caught in about genetic evidence:

      Dawkins Claimed Best Evidence For Evolution Refuted - video
      http://www.youtube.com/watch?v=IfFZ8lCn5uU

      The false claim from Dawkins' own mouth is noted here:

      Dawkins Caught Lying for Darwin - video
      http://www.youtube.com/watch?v=vnYik52Y5rI

      Delete
    8. ba77's gullibility knows no limits. He will cite any fool who is against evolution.

      How do you like Kevin Hovind, ba?

      Delete
    9. So oleq it does not matter that Dawkins was caught blatantly misrepresenting the genetic evidence in your book? It only matters that you don't respect the YEC position and that you use that as ad hominem. And your a-priori dogmatic neo-Darwinism should not count as ad hominem against you because why exactly???

      Delete
    10. "Respect the YEC position?" For what? For being totally out of whack with astronomy, physics, geology, and biology? I have no respect for fools.

      Delete
    11. Actually oleq, I find atheistic neo-Darwinists to be completely out of whack with what biology (as in rationalizing away the draw dropping complexity now being revealed in biology), physics (as in rationalizing away what the second law clearly implies for neo-Darwinism), geology (as in rationalizing away many unexplained catastrophic events revealed in geology) and astronomy (as in denying or completely ignoring the clear Theistic implications of the Big Bang and of extreme fine-tuning).

      Thus why the hypocrisy???

      Delete
    12. ba77, but you don't know much biology, physics, or geology. Your faith is the source of your knowledge.

      Delete
    13. For instance, you just mentioned the second law (of thermodynamics, I presume) and neo-Darwinism. That's why Dembski had to invent a "fourth law" of thermodynamics.

      Delete
    14. ba77: The false claim from Dawkins' own mouth is noted here:

      Dawkins Caught Lying for Darwin - video
      http://www.youtube.com/watch?v=vnYik52Y5rI


      First of all, ba77, a lie is a deliberate untruth. So to support your claim that Dawkins is lying here, you would have to a) show that what he is saying is untrue and b) that he knows it to be true.

      Fortunately, a) is false, so we don't have to proceed to b).

      Dawkins is not lying. He is, of course, referring to the coding sequence of the gene (the exons), not the non-coding introns.

      And according to this Nature paper:

      We compared the FOXP2 protein structures predicted by a variety of methods6 for humans, chimpanzees, orang-utans and mice. Whereas the chimpanzee and mouse structures were essentially identical and the orang-utan showed only a minor change in secondary structure, the human-specific change at position 325 creates a potential target site for phosphorylation by protein kinase C together with a minor change in predicted secondary structure. Several studies have shown that phosphorylation of forkhead transcription factors can be an important mechanism mediating transcriptional regulation7, 8. Thus, although the FOXP2 protein is extremely conserved among mammals, it acquired two amino-acid changes on the human lineage, at least one of which may have functional consequences. This is an intriguing finding, because FOXP2 is the first gene known to be involved in the development of speech and language.

      My bold.

      Two amino acid changes would amount, at most, to 6 differences, although there could be variant "spellings". "About 9" seems consistent with this evidence.

      Delete
    15. Hmmm, but how many changes can neo-Darwinian processes account for?

      You can't even empirically demonstrate the fixation of a single unambiguously beneficial mutation in a multicellular creature!

      Experimental Evolution in Fruit Flies (35 years of trying to force fruit flies to evolve in the laboratory fails, spectacularly) - October 2010
      Excerpt: "Despite decades of sustained selection in relatively small, sexually reproducing laboratory populations, selection did not lead to the fixation of newly arising unconditionally advantageous alleles.,,, "This research really upends the dominant paradigm about how species evolve," said ecology and evolutionary biology professor Anthony Long, the primary investigator.
      http://www.arn.org/blogs/index.php/literature/2010/10/07/experimental_evolution_in_fruit_flies

      Moreover,,,

      More from Ann Gauger on why humans didn’t happen the way Darwin said - July 2012
      Excerpt: Each of these new features probably required multiple mutations. Getting a feature that requires six neutral mutations is the limit of what bacteria can produce. For primates (e.g., monkeys, apes and humans) the limit is much more severe. Because of much smaller effective population sizes (an estimated ten thousand for humans instead of a billion for bacteria) and longer generation times (fifteen to twenty years per generation for humans vs. a thousand generations per year for bacteria), it would take a very long time for even a single beneficial mutation to appear and become fixed in a human population.
      You don’t have to take my word for it. In 2007, Durrett and Schmidt estimated in the journal Genetics that for a single mutation to occur in a nucleotide-binding site and be fixed in a primate lineage would require a waiting time of six million years. The same authors later estimated it would take 216 million years for the binding site to acquire two mutations, if the first mutation was neutral in its effect.
      Facing Facts
      But six million years is the entire time allotted for the transition from our last common ancestor with chimps to us according to the standard evolutionary timescale. Two hundred and sixteen million years takes us back to the Triassic, when the very first mammals appeared. One or two mutations simply aren’t sufficient to produce the necessary changes— sixteen anatomical features—in the time available. At most, a new binding site might affect the regulation of one or two genes.
      http://www.uncommondescent.com/intelligent-design/more-from-ann-gauger-on-why-humans-didnt-happen-the-way-darwin-said/

      Delete
    16. But the changes neo-Darwinism must account for a far greater than even the severe limit that Dr. Gauger conceded:

      From Jerry Coyne, More Table-Pounding, Hand-Waving - May 2012
      Excerpt: "More than 6 percent of genes found in humans simply aren't found in any form in chimpanzees. There are over fourteen hundred novel genes expressed in humans but not in chimps."
      Jerry Coyne - ardent and 'angry' neo-Darwinist - professor at the University of Chicago in the department of ecology and evolution for twenty years. He specializes in evolutionary genetics.

      Could Chance Arrange the Code for (Just) One Gene?
      "our minds cannot grasp such an extremely small probability as that involved in the accidental arranging of even one gene (10^-236)."
      http://www.creationsafaris.com/epoi_c10.htm

      Moreover the 'anomaly' of unique ORFan genes is found in every new genome sequenced:

      Widespread ORFan Genes Challenge Common Descent – Paul Nelson – video with references
      http://www.vimeo.com/17135166

      Genomes of similar species - Cornelius Hunter PhD.
      Excerpt: Different variants of the Escherichia coli bacteria, for instance, each have hundreds of unique genes. And some of these genes have been found to have important functions, such as helping to construct proteins. [8]
      Massive genetic differences were also found between different fruit fly species. The fruit fly is one of the most intensely researched organisms and in recent years a systematic study of the genomes of a dozen different species was undertaken. Evolutionists were surprised to find novel features in the genomes of each of these different fruit fly species. Thousands of genes showed up missing in many of the species, and some genes showed up in only a single species. [9] As one science writer put it, “an astonishing 12 per cent of recently evolved genes in fruit flies appear to have evolved from scratch.” [10] These so-called novel genes would have had to have evolved over a few million years—a time period previously considered to allow only for minor genetic changes. [11,12] ,,, etc.. etc…
      http://www.darwinspredictions.com/#_4.2_Genomes_o

      Delete
    17. As alluded to above, completely contrary to evolutionary thought, these 'new' ORFan genes are found to be just as essential as 'old' genes for maintaining life:

      Age doesn't matter: New genes are as essential as ancient ones - December 2010
      Excerpt: "A new gene is as essential as any other gene; the importance of a gene is independent of its age," said Manyuan Long, PhD, Professor of Ecology & Evolution and senior author of the paper. "New genes are no longer just vinegar, they are now equally likely to be butter and bread. We were shocked."
      http://www.sciencedaily.com/releases/2010/12/101216142523.htm

      New genes in Drosophila quickly become essential. - December 2010
      Excerpt: The proportion of genes that are essential is similar in every evolutionary age group that we examined. Under constitutive silencing of these young essential genes, lethality was high in the pupal (later) stage and (but was) also found in the larval (early) stages.
      http://www.sciencemag.org/content/330/6011/1682.abstract

      related notes:

      The Extreme Complexity Of Genes - Dr. Raymond G. Bohlin - video
      http://www.metacafe.com/watch/8593991/

      De Novo Origin of Human Protein-Coding Genes - November 10, 2011
      Excerpt: The de novo origin of a new protein-coding gene from non-coding DNA is considered to be a very rare occurrence in genomes. Here we identify 60 new protein-coding genes that originated de novo on the human lineage since divergence from the chimpanzee. The functionality of these genes is supported by both transcriptional and proteomic evidence.,,,
      Here we identify 60 new protein-coding genes that originated de novo on the human lineage since divergence from the chimpanzee, supported by both transcriptional and proteomic evidence. It is inconsistent with the traditional view that the de novo origin of new genes is rare.
      http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002379;jsessionid=0ADFB2D28FD590F0785D9A7D2D1D4569

      Delete
    18. ba77 goes into Gish gallop.

      Delete
    19. My comment above is missing a sentence in the middle. Second try:

      For instance, you just mentioned the second law (of thermodynamics, I presume) and neo-Darwinism. These have nothing to do with each other, despite the silly rantings of Granville Sewell (who is not a physicist). That's why Dembski had to invent a "fourth law" of thermodynamics.

      Delete
    20. And here we see the world-champion goal-post mover at his inimitable best:

      Hmmm, but how many changes can neo-Darwinian processes account for?

      Your assertion, ba77, was that Dawkins was lying. I demonstrated that he was not, backing my own claim up with an actual citation.

      You are very prone to accuse others of lying (when in fact, at best, all you have is the conviction that they are in error, which is not the same thing). When asked to support your claim that what they have said is untrue...

      ...you change the subject.

      It makes your case look bad, ba77.

      As for how a Darwinian process can account for two amino acid changes - what is the problem? it's exactly the kind of change that Darwinian processes excel at - small changes in DNA sequence with small effects on a protein that have phenotypic effects that benefit the organism.

      Delete
    21. ba77: really, it's OK. It doesn't makes difference to the case for God whether evolutionary theory is true or not. Or, at any rate, evolutionary theory is completely compatible with theism, although not with a literal interpretation of the bible.

      You won't turn into an atheist overnight. Ken Miller himself is a devout Christian.

      Calm down.

      Delete
    22. "For instance, you just mentioned the second law (of thermodynamics, I presume) and neo-Darwinism. That's why Dembski had to invent a "fourth law" of thermodynamics."

      It can only be by force of willful denial, that the implications of the second law (of thermodynamics: Entropy) for biology are not clearly understood by neo-Darwinists:

      The evidence for the detrimental nature of mutations in humans is overwhelming for scientists have already cited over 100,000 mutational disorders.

      Inside the Human Genome: A Case for Non-Intelligent Design - Pg. 57 By John C. Avise
      Excerpt: "Another compilation of gene lesions responsible for inherited diseases is the web-based Human Gene Mutation Database (HGMD). Recent versions of HGMD describe more than 75,000 different disease causing mutations identified to date in Homo-sapiens."

      I went to the mutation database website cited by John Avise and found:

      HGMD®: Now celebrating our 100,000 mutation milestone!
      http://www.hgmd.org/

      We Are All Mutants: First Direct Whole-Genome Measure of Human Mutation Predicts 60 New Mutations in Each of Us - June 2011
      http://www.sciencedaily.com/releases/2011/06/110613012758.htm

      Here's a interesting talk by Dr. John Sanford. Starting at the 17 minute mark going to the 22 minute mark. He relates how slightly detrimental mutations, that accumulate each time a cell divides, are the primary reason why our physical/material bodies grow old and die.

      John Sanford on (Genetic Entropy) - Down, Not Up - 2-4-2012 (at Loma Linda University) - video
      http://www.youtube.com/watch?v=PHsu94HQrL0

      Notes from John Sanford's preceding video:

      *3 new mutations every time a cell divides in your body
      * Average cell of 15 year old has up to 6000 mutations
      *Average cell of 60 year old has 40,000 mutations
      Reproductive cells are 'designed' so that, early on in development, they are 'set aside' and thus they do not accumulate mutations as the rest of the cells of our bodies do. Regardless of this protective barrier against the accumulation of slightly detrimental mutations still we find that,,,
      *60-175 mutations are passed on to each new generation.

      Here are the papers cited by Dr. Sanford in the preceding video at the 24:40 minute mark:

      The high spontaneous mutation rate: Is it a health risk?* - James F. Crow - 1997
      Excerpt: If war or famine force our descendants to return to a stone-age life they will have to contend with all the problems that their stone-age ancestors had plus mutations that have accumulated in the meantime.
      http://www.pnas.org/content/94/16/8380.full

      Delete
    23. Contamination of the genome by very slightly deleterious mutations:
      why have we not died 100 times over? Kondrashov A.S.
      http://www.ingentaconnect.com/content/ap/jt/1995/00000175/00000004/art00167

      Why are we still alive? - LAURENCE LOEWE - Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, - 2006
      Excerpt: In the last few years evolution@home has accumulated over 100 years of computing time in its quest for a better understanding of the consequences of mutations that are slightly harmful and therefore might not be removed from populations by natural selection.,,, Results show that this may be less than 20 million years, resulting in a genomic decay paradox, since mitochondria in the human line are (presupposed to be) older.
      http://www.evolutionary-research.net/news/2008/04/01/why-are-we-still-alive

      Rate, molecular spectrum, and consequences of human mutation - Michael Lynch - 2009
      Excerpt: Thus, although there is considerable uncertainty in the preceding numbers, it is difficult to escape the conclusion that the per-generation reduction in fitness due to recurrent mutation is at least 1% in humans and quite possibly as high as 5%.
      http://www.pnas.org/content/107/3/961.full

      Interestingly, this ‘slightly detrimental’ mutation rate of 100 to 200, or even 60, per generation is far greater than what even evolutionists agree is an acceptable mutation rate since detrimental mutations will accumulate far faster than ‘selection’ can eliminate them in any given genome:

      Human evolution or extinction - discussion on acceptable mutation rate per generation (with clips from Dr. John Sanford) - video
      http://www.youtube.com/watch?v=aC_NyFZG7pM

      Beyond A 'Speed Limit' On Mutations, Species Risk Extinction
      Excerpt: Shakhnovich's group found that for most organisms, including viruses and bacteria, an organism's rate of genome mutation must stay below 6 mutations per genome per generation to prevent the accumulation of too many potentially lethal changes in genetic material.
      http://www.sciencedaily.com/releases/2007/10/071001172753.htm

      Genetic Entropy - Dr. John Sanford - Evolution vs. Entropic Reality - video (Notes in description)
      http://vimeo.com/35088933

      Using Computer Simulation to Understand Mutation Accumulation Dynamics and Genetic Load:
      Excerpt: We apply a biologically realistic forward-time population genetics program to study human mutation accumulation under a wide-range of circumstances.,, Our numerical simulations consistently show that deleterious mutations accumulate linearly across a large portion of the relevant parameter space.
      http://bioinformatics.cau.edu.cn/lecture/chinaproof.pdf
      MENDEL’S ACCOUNTANT: J. SANFORD†, J. BAUMGARDNER‡, W. BREWER§, P. GIBSON¶, AND W. REMINE
      http://mendelsaccount.sourceforge.net

      Delete
    24. Dawkins claim was that it was the best evidence for human evolution and yet his claim was shown to be false. The citations, 11 of them, demonstrating are listed by the publisher of the video I listed. Do you want to me to cite that for you to?

      Delete
    25. Dismount your Gish horse for a moment, ba77, and stay with me. Expand a bit on the second law of thermodynamics, will ya? This is a subject I know well enough to teach at the graduate level. Should be fun.

      Delete
    26. Dismount your Gish horse for a moment, ba77, and stay with me. Expand a bit on the second law of thermodynamics, will ya?

      I'll do that as soon as you empirically show me a mutation rate that is not completely antagonistic to the neo-Darwinian framework! Elsewise you are not even in the realm of rigorous science!

      The following study surveys four decades of experimental work, and solidly backs up the preceding conclusion that there has never been an observed violation of genetic entropy:

      “The First Rule of Adaptive Evolution”: Break or blunt any functional coded element whose loss would yield a net fitness gain - Michael Behe - December 2010
      Excerpt: In its most recent issue The Quarterly Review of Biology has published a review by myself of laboratory evolution experiments of microbes going back four decades.,,, The gist of the paper is that so far the overwhelming number of adaptive (that is, helpful) mutations seen in laboratory evolution experiments are either loss or modification of function. Of course we had already known that the great majority of mutations that have a visible effect on an organism are deleterious. Now, surprisingly, it seems that even the great majority of helpful mutations degrade the genome to a greater or lesser extent.,,, I dub it “The First Rule of Adaptive Evolution”: Break or blunt any functional coded element whose loss would yield a net fitness gain.(that is a net 'fitness gain' within a 'stressed' environment i.e. remove the stress from the environment and the parent strain is always more 'fit')
      http://behe.uncommondescent.com/2010/12/the-first-rule-of-adaptive-evolution/

      Michael Behe talks about the preceding paper on this podcast:

      Michael Behe: Challenging Darwin, One Peer-Reviewed Paper at a Time - December 2010
      http://intelligentdesign.podomatic.com/player/web/2010-12-23T11_53_46-08_00

      Are You Looking for the Simplest and Clearest Argument for Intelligent Design? - Granville Sewell (2nd Law) - video
      http://www.evolutionnews.org/2012/02/looking_for_the056711.html

      Where's the substantiating evidence for neo-Darwinism?
      https://docs.google.com/document/d/1q-PBeQELzT4pkgxB2ZOxGxwv6ynOixfzqzsFlCJ9jrw/edit

      Delete
    27. Dawkins claim was that it was the best evidence for human evolution and yet his claim was shown to be false. The citations, 11 of them, demonstrating are listed by the publisher of the video I listed. Do you want to me to cite that for you to?

      Well, it was the one that he eventually said he find particularly convincing, but he starts by pointing out that it's the consilience of many lines of evidence that makes the case, not one piece of the puzzle. And it is a particularly good piece of evidence.

      And his claim was NOT shown to be false - I have just linked to the Nature paper that he is probably thinking of, which indicates only a handful of differences between the FOXP gene in humans and in other great apes.

      The idiot who made that video stupidly chose to assume that Dawkins was including the non-coding portions of the gene - the introns. Clearly he was not, and it would have made no sense for him to do that. It is only the coding parts that will be conserved.

      Delete
    28. ba77, you have made a claim that the second law of thermodynamics contradicts neo-Darwinism. Defend it or retract it.

      Delete
    29. Cite a mutation rate that is in disagreement with the implications of the second law!

      Moreover:

      Blackholes - The neo-Darwinian ‘god of entropic randomness’ which can create all things (at least according to them)

      Being the helpful guy I am, always trying to help atheists out when I get a chance, I’ve been trying to piece together a experiment that would prove once and for all, for everyone to see, that RANDOM variation plus undirected natural selection can produce functional proteins just as atheists adamantly claim (even though no one has ever seen RANDOM processes do this). Now I just about got the RANDOM part of the experiment down for the atheists! I’ve searched for the maximum source of randomness that I could find in the universe, (since the 'god of randomness' is who atheists adamantly claim for their creator), and I think I’ve found their god for them;

      First:

      Evolution is a Fact, Just Like Gravity is a Fact! UhOh! - January 2010
      Excerpt: The results of this paper suggest gravity arises as an entropic force, once space and time themselves have emerged.
      http://www.uncommondescent.com/intelligent-design/evolution-is-a-fact-just-like-gravity-is-a-fact-uhoh/

      Thermodynamics – 3.1 Entropy
      Excerpt:
      Entropy – A measure of the amount of randomness
      or disorder in a system.
      http://www.saskschools.ca/curr_content/chem30_05/1_energy/energy3_1.htm

      Thus, the more entropy a system has the more randomness it will generate for our experiment to find a RANDOM functional protein. And if we ask, ‘what is the maximum source of entropy, i.e. RANDOMNESS, in the universe?’, we find this:

      Entropy of the Universe – Hugh Ross – May 2010
      Excerpt: Egan and Lineweaver found that supermassive black holes are the largest contributor to the observable universe’s entropy. They showed that these supermassive black holes contribute about 30 times more entropy than what the previous research teams estimated.
      http://www.reasons.org/entropy-universe

      “But why was the big bang so precisely organized, whereas the big crunch (or the singularities in black holes) would be expected to be totally chaotic? It would appear that this question can be phrased in terms of the behaviour of the WEYL part of the space-time curvature at space-time singularities. What we appear to find is that there is a constraint WEYL = 0 (or something very like this) at initial space-time singularities-but not at final singularities-and this seems to be what confines the Creator’s choice to this very tiny region of phase space.”
      Roger Penrose - How Special Was The Big Bang?

      Plus for a added bonus for atheists, being the helpful guy that I am, I found that if we find a massive magnetized blackhole we might just start to overcome the homochirality problem, which is a huge problem against finding functional proteins, as well:

      Homochirality and Darwin: part 2 – Robert Sheldon – May 2010
      Excerpt: With regard to the deniers who think homochirality is not much of a problem, I only ask whether a solution requiring multiple massive magnetized black-hole supernovae doesn’t imply there is at least a small difficulty to overcome? A difficulty, perhaps, that points to the non-random nature of life in the cosmos?
      http://procrustes.blogtownhall.com/page3

      Delete
    30. But of course there is the extreme logistics problem with actually transporting the atheists to the massive magnetized blackholes to actually do the experiments, so that they may try to actually RANDOMLY generate a functional protein just as they claim can be done. Not to mention the minor problem of someone trying to survive being stretched into as a piece of spaghetti, by the extreme warping of space-time, near the blackhole.
      What Would Happen If You Fell into a Black Hole? - video
      http://www.youtube.com/watch?v=gLMiJQXsmkc

      ,,Not to mention trying to survive the extremely high temperatures surrounding the event horizon of the black hole:,,

      Scientists gear up to take a picture of a black hole - January 2012
      Excerpt: "Swirling around the black hole like water circling the drain in a bathtub, the matter compresses and the resulting friction turns it into plasma heated to a billion degrees or more, causing it to 'glow' – and radiate energy that we can detect here on Earth."
      http://www.physorg.com/news/2012-01-scientists-gear-picture-black-hole.html

      But what the hey, it is just a little sacrifice for ‘science’ right!?! At least atheists will have the maximum source of randomness in the universe to work with in their experiments!!! But there is another problem I probably need to tell atheists about before they pack up and go off to the massive magnetized blackholes in order to prove to the world that their ‘god of randomness’ can create all things,

      “Gain in entropy always means loss of information, and nothing more.”
      Gilbert Newton Lewis – Eminent Chemist

      “Is there a real connection between entropy in physics and the entropy of information? ….The equations of information theory and the second law are the same, suggesting that the idea of entropy is something fundamental…”
      Tom Siegfried, Dallas Morning News, 5/14/90 – Quotes attributed to Robert W. Lucky, Ex. Director of Research, AT&T, Bell Laboratories & John A. Wheeler, of Princeton & Univ. of TX, Austin in the article
      http://www.bible.ca/tracks/dp-lawsScience.htm

      But what the hey, atheists haven't needed any stinking equations to prove their theory so far have they!?!

      Oxford University Admits Darwinism's Shaky Math Foundation - May 2011
      Excerpt: However, mathematical population geneticists mainly deny that natural selection leads to optimization of any useful kind. This fifty-year old schism is intellectually damaging in itself, and has prevented improvements in our concept of what fitness is. - On a 2011 Job Description for a Mathematician, at Oxford, to 'fix' the persistent mathematical problems with neo-Darwinism within two years.
      http://www.evolutionnews.org/2011/05/oxford_university_admits_darwi046351.html

      I even have a inspirational quote for the future experiment of our space traveling atheists;

      GILBERT NEWTON LEWIS: AMERICAN CHEMIST (1875-1946)
      “I have attempted to give you a glimpse…of what there may be of soul in chemistry. But it may have been in vain. Perchance the chemist is already damned and the guardian the blackest. But if the chemist has lost his soul, he will not have lost his courage and as he descends into the inferno, sees the rows of glowing furnaces and sniffs the homey fumes of brimstone, he will call out-: ‘Asmodeus, hand me a test-tube.’”(1) Gilbert Newton Lewis
      http://www.woodrow.org/teachers/ci/1992/Lewis.html

      And I even have a inspirational song for their experiment;

      Creed – Six Feet
      http://www.youtube.com/v/aQ9GrZ3CEyY&fs=1&source=uds&autoplay=1

      Delete
    31. No, ba77. You first have to explain how the second law of thermodynamics contradicts neo-Darwinism. You have made that claim. Defend it or retract it.

      Delete
    32. No Oleq, you have to defend the claim that neo-Darwinism is not in severe conflict with the clear implications of the second law. I don't have to do anything other than note that the overwhelming slightly detrimental mutation rate that is found is exactly what we expect from the implications of the second law. You are the one making the extraordinary claim that the implications of the second law do not hold for biology, thus you must produce extraordinary evidence that biology is exempt!! I merely have to note there is concordance between the mutation rate and the second law!

      Evolution Vs Genetic Entropy - Andy McIntosh - video
      http://www.metacafe.com/watch/4028086

      Related note:

      The Law of Physicodynamic Insufficiency - Dr David L. Abel - November 2010
      Excerpt: “If decision-node programming selections are made randomly or by law rather than with purposeful intent, no non-trivial (sophisticated) function will spontaneously arise.”,,, After ten years of continual republication of the null hypothesis with appeals for falsification, no falsification has been provided. The time has come to extend this null hypothesis into a formal scientific prediction: “No non trivial algorithmic/computational utility will ever arise from chance and/or necessity alone.”
      http://www-qa.scitopics.com/The_Law_of_Physicodynamic_Insufficiency.html

      Delete
    33. ba77: No Oleq, you have to defend the claim that neo-Darwinism is not in severe conflict with the clear implications of the second law. I don't have to do anything other than note that the overwhelming slightly detrimental mutation rate that is found is exactly what we expect from the implications of the second law.

      None of the standard formulations of the 2nd law has anything to do with the rate of biological mutations. Therefore the burden is on you to establish that it presents a problem for neo-Darwinism. Go ahead and do that. Or retract your claim.

      Delete
    34. No oleq the burden is on you to show that your extraordinary claim that biology is somehow exempt from the 'universal' decaying effects of thermodynamics is coherent. I have already EMPIRICALLY shown (which is the strongest form of proof in science) strong concordance with a overwhelmingly slightly detrimental mutation rate to the decaying effects of entropy we witness all around us everyday! or to put it in the words of David Berlinski, "we have a devilishly hard time finding any truly beneficial mutations whatsoever',,, Go figure!!! I certainly am not going to retract the clear implications of the second law towards biology in the face of your inconcordant dogmatism especially when you have no empirical backing to which you can appeal!!!

      Delete
    35. ba77,

      The "'universal' decaying effects of thermodynamics" is a fairy tale propagated by creationists. No rigorous statement of the 2nd law contains anything of the sort. Here are a couple:

      Clausius's statement: No process is possible whose sole result is the transfer of heat from a body of lower temperature to a body of higher temperature.

      Kelvin's statement: No process is possible in which the sole result is the absorption of heat from a reservoir and its complete conversion into work.

      Statistical mechanics: Entropy of a closed system cannot decrease.

      Take any of these statements (as opposed to silly pop versions) and show how they contradict neo-Darwinism. (Hint: you can't. No creationist has yet succeeded in doing so.)

      Delete
    36. Who are we going to believe oleq or our own eyes:

      Ageing Process in 40 seconds - video
      http://www.youtube.com/watch?v=hSdxYmGro_Y

      John Sanford on (Genetic Entropy) – Down, Not Up – 2-4-2012 (lecture at Loma Linda University) – video
      http://www.youtube.com/watch?v=PHsu94HQrL0

      Notes from John Sanford’s preceding lecture:

      *3 new mutations every time a cell divides in your body
      * Average cell of 15 year old has up to 6000 mutations
      *Average cell of 60 year old has 40,000 mutations
      Reproductive cells are ‘designed’ so that, early on in development, they are ‘set aside’ and thus they do not accumulate mutations as the rest of the cells of our bodies do. Regardless of this protective barrier against the accumulation of slightly detrimental mutations still we find that,,,
      *60-175 mutations are passed on to each new generation.

      Psalm 102:25-27
      Of old You laid the foundation of the earth, And the heavens are the work of Your hands. They will perish, but You will endure; Yes, they will all grow old like a garment; Like a cloak You will change them, And they will be changed. But You are the same, And Your years will have no end.

      As to a technical discussion:

      Physicist Rob Sheldon offers some thoughts on Sal Cordova vs. Granville Sewell on 2nd Law Thermo - July 2012
      http://www.uncommondescent.com/intelligent-design/physicist-rob-sheldon-offers-some-thoughts-on-sal-cordova-vs-granville-sewell-on-2nd-law-thermo/

      Now oleq as to you proving that the implications of the second law are not binding to biology, and to humans in particular, you merely have to show someone who is completely immune to aging effects on the their body and more importantly immune to bodily death! But that defying death proof you must deal with sounds eerily similar to the Christian claimed proof for the resurrection of Christ!

      The Center Of The Universe Is Life - General Relativity, Quantum Mechanics, Entropy and The Shroud Of Turin - video
      http://vimeo.com/34084462

      Turin Shroud Enters 3D Age - Pictures, Articles and Videos
      https://docs.google.com/document/pub?id=1gDY4CJkoFedewMG94gdUk1Z1jexestdy5fh87RwWAfg

      Condensed notes on The Authenticity of the Shroud of Turin
      https://docs.google.com/document/d/15IGs-5nupAmTdE5V-_uPjz25ViXbQKi9-TyhnLpaC9U/edit

      Delete
    37. Of note from physicist Rob Sheldon's article:

      Physicist Rob Sheldon offers some thoughts on Sal Cordova vs. Granville Sewell on 2nd Law Thermo - July 2012
      Excerpt: The Equivalence: Boltzmann’s famous equation (and engraved on his tombstone) S = k ln W, merely is an exchange rate conversion. If W is lira, and S is dollars, then k ln() is the conversion of the one to the other, which is empirically determined. Boltzmann’s constant “k” is a semi-empirical conversion number that made Gibbs “stat mech” definition work with the earlier “thermo” definition of Lord Kelvin and co.
      Despite this being something as simple as a conversion factor, you must realize how important it was to connect these two. When Einstein connected mass to energy with E = (c2) m, we can now talk about mass-energy conservation, atom bombs and baby universes, whereas before Einstein they were totally different quantities.
      Likewise, by connecting the two things, thermodynamics and statistical mechanics, then the hard rules derived from thermo can now be applied to statistics of counting permutations.
      This is where Granville derives the potency of his argument, since a living organism certainly shows unusual permutations of the atoms, and thus has stat mech entropy that via Boltzmann, must obey the 2nd law. If life violates this, then it must not be lawfully possible for evolution to happen (without an input of work or information.)
      The one remaining problem, is how to calculate it precisely (how to calculate the entropy precisely).
      note: (Dr. Sheldon goes on to say that because it is extremely difficult to calculate entropy precisely for living cells, this is exactly where Darwinists try to claim evolution does not violate the second law. Yet regardless of the games Darwinists play because of this lack of mathematical precision, for all intents and purposes (and common sense) as far as we can ascertain, for evolution to occur would indeed violate the 'iron clad' second law of thermodynamics!)
      http://www.uncommondescent.com/intelligent-design/physicist-rob-sheldon-offers-some-thoughts-on-sal-cordova-vs-granville-sewell-on-2nd-law-thermo/

      Delete
    38. While we are on the topic; It is interesting to point out just how far out of thermodynamic equilibrium a 'simple' cell is:

      Professor Harold Morowitz shows the Origin of Life ‘problem’ escalates dramatically over the 1 in 10^40,000 figure when working from a thermodynamic perspective,:

      “The probability for the chance of formation of the smallest, simplest form of living organism known is 1 in 10^340,000,000. This number is 10 to the 340 millionth power! The size of this figure is truly staggering since there is only supposed to be approximately 10^80 (10 to the 80th power) electrons in the whole universe!”
      (Professor Harold Morowitz, Energy Flow In Biology pg. 99, Biophysicist of George Mason University)

      Dr. Morowitz did another probability calculation working from the thermodynamic perspective with a already existing cell and came up with this number:

      DID LIFE START BY CHANCE?
      Excerpt: Molecular biophysicist, Horold Morowitz (Yale University), calculated the odds of life beginning under natural conditions (spontaneous generation). He calculated, if one were to take the simplest living cell and break every chemical bond within it, the odds that the cell would reassemble under ideal natural conditions (the best possible chemical environment) would be one chance in 10^100,000,000,000. You will have probably have trouble imagining a number so large, so Hugh Ross provides us with the following example. If all the matter in the Universe was converted into building blocks of life, and if assembly of these building blocks were attempted once a microsecond for the entire age of the universe. Then instead of the odds being 1 in 10^100,000,000,000, they would be 1 in 10^99,999,999,916 (also of note: 1 with 100 billion zeros following would fill approx. 20,000 encyclopedias)
      http://members.tripod.com/~Black_J/chance.html

      Punctured cell will never reassemble – Jonathan Wells – 2:40 mark of video
      http://www.youtube.com/watch?v=WKoiivfe_mo

      The information content that is derived to be in a cell when working from a purely thermodynamic perspective is simply astonishing to ponder:

      ‘The information content of a simple cell has been estimated as around 10^12 bits, comparable to about a hundred million pages of the Encyclopedia Britannica.”
      Carl Sagan, “Life” in Encyclopedia Britannica: Macropaedia (1974 ed.), pp. 893-894

      “a one-celled bacterium, e. coli, is estimated to contain the equivalent of 100 million pages of Encyclopedia Britannica. Expressed in information in science jargon, this would be the same as 10^12 bits of information. In comparison, the total writings from classical Greek Civilization is only 10^9 bits, and the largest libraries in the world – The British Museum, Oxford Bodleian Library, New York Public Library, Harvard Widenier Library, and the Moscow Lenin Library – have about 10 million volumes or 10^12 bits.” – R. C. Wysong

      For calculations for information, when working from the thermodynamic perspective, please see the following site:

      Moleular Biophysics – Information theory. Relation between information and entropy: – Setlow-Pollard, Ed. Addison Wesley
      Excerpt: Linschitz gave the figure 9.3 x 10^12 cal/deg or 9.3 x 10^12 x 4.2 joules/deg for the entropy of a bacterial cell. Using the relation H = S/(k In 2), we find that the information content is 4 x 10^12 bits. Morowitz’ deduction from the work of Bayne-Jones and Rhees gives the lower value of 5.6 x 10^11 bits, which is still in the neighborhood of 10^12 bits. Thus two quite different approaches give rather concordant figures.
      http://www.astroscu.unam.mx/~angel/tsb/molecular.htm

      And all this begs the question of, since purely matter and energy, working on there own, can soon return a organism to thermodynamic equilibrium, just what is constraining living organisms, besides matter and energy, to be so far out of thermodynamic equilibrium in the first place?

      Delete
    39. ba77,

      I am not interested in the copied-and-pasted responses you provide. Give me a concise answer, in your own words, to this question: how do you get from the second law of thermodynamics—in any of its standard formulations—to the impossibility of neo-Darwinism.

      In fact, you acknowledge (along with NASA engineer Sheldon) that you don't know how to calculate the entropy change in living cells and yet insist that there is a 2nd-law violation anyway. On what grounds?

      Furthermore, it is silly to appeal to "your own eyes" on questions like a change in entropy. Your eyes can't measure the amount of entropy.

      You can continue to wriggle like worm or you can concede that you have no grounds to claim violation of the 2nd law of thermodynamics by theory of evolution. None.

      Delete
    40. oleq, you are the one making the extraordinary claim that the second law does not hold for biology! The plain fact is that you have provided ZERO empirical evidence that entropy does not hold for biology whereas I provided many links and cites pointing out that genomes are in a long slow process of degeneration just exactly as would be expected if the law did hold! Moreover, This following comment of yours is simply ludicrous:

      "Furthermore, it is silly to appeal to "your own eyes" on questions like a change in entropy."

      Everyone of us is growing old and dying due to the accumulation of slightly detrimental mutations in our cells. This is a undeniable fact. Everyone can see the effects of entropy intimately because we are each personally living through the effects of entropy on own material bodies. Your denial of this plain 'common sense' fact that is painfully apparent to the majority of common sense Americans who don't buy your Darwinian hogwash, is clear evidence of the levels of denial, and imagination, that neo-Darwinists will resort just so as to protect their atheism. Clue for you, the answer to this inescapable 'death dilemma' that entropy presents personally to each of us is behind door #1 oleq!

      John 10:9
      I am the door: by me if any man enter in, he shall be saved, and shall go in and out, and find pasture.

      John 11:26
      and whoever lives and believes in me will never die. Do you believe this?"

      Natalie Grant - Alive (Resurrection music video)
      http://www.godtube.com/watch/?v=KPYWPGNX

      Delete
    41. ba77: oleq, you are the one making the extraordinary claim that the second law does not hold for biology!

      I am not.

      ba77: Everyone of us is growing old and dying due to the accumulation of slightly detrimental mutations in our cells. This is a undeniable fact. Everyone can see the effects of entropy intimately because we are each personally living through the effects of entropy on own material bodies.

      This has nothing to do with entropy.

      ba77: Your denial of this plain 'common sense' fact that is painfully apparent to the majority of common sense Americans who don't buy your Darwinian hogwash, is clear evidence of the levels of denial, and imagination, that neo-Darwinists will resort just so as to protect their atheism.

      "Common sense" does not equal science. Decay of biological material has nothing to do with entropy. It's a popular misconception.

      So we're back to Square 1. You can't get from the 2nd law of thermodynamics to the impossibility of neo-Darwinism in a logical way. There is simply no path. You have to invoke a silly caricature of the 2nd law in order to do that. So garbage in, garbage out.

      And stop calling me "oleq."

      Delete
    42. "ba77: oleq, you are the one making the extraordinary claim that the second law does not hold for biology!

      I am not."

      and round you go chasing your tail,, Okie Dokie please show me your exact empirical evidence that entropy, in the form of Genetic Entropy is not true and that evolution , as in overcoming that cliff wall of slightly detrimental mutations, is true. I've already listed several cites for my side, convincing proof for your side that entropy does not hold for biology would look something like perhaps a single functional protein being generated by purely material processes (for a bare minimum start as to establishing your basis in science!)!

      notes:

      Abiogenic Origin of Life: A Theory in Crisis - Arthur V. Chadwick, Ph.D.
      Excerpt: A thermodynamic analysis of a mixture of protein and amino acids in an ocean containing a 1 molar solution of each amino acid (100,000,000 times higher concentration than we inferred to be present in the prebiological ocean) indicates the concentration of a protein containing just 100 peptide bonds (101 amino acids) at equilibrium would be 10^-338 molar. Just to make this number meaningful, our universe may have a volume somewhere in the neighborhood of 10^85 liters. At 10^-338 molar, we would need an ocean with a volume equal to 10^229 universes (100, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000) just to find a single molecule of any protein with 100 peptide bonds. So we must look elsewhere for a mechanism to produce polymers. It will not happen in the ocean.
      http://origins.swau.edu/papers/life/chadwick/default.html

      Good luck with all that oleg

      Delete
    43. ba77: Okie Dokie please show me your exact empirical evidence that entropy, in the form of Genetic Entropy is not true

      First, you need to explain what "genetic entropy" is and how it is related to the 2nd law of thermodynamics. No copying and pasting. Use your own words. Show all your work. :)

      Delete
    44. ba77, if you link to another YEC site I am going to die of laughter and you will win by default. No fair.

      Delete
    45. No oleq, you are the one making the extraordinary claim that biology is somehow immune to the effects of entropy. i.e. you actually have to show empirical evidence of Darwinian evolution!!!

      Good luck with that!

      Where's the substantiating evidence for neo-Darwinism?
      https://docs.google.com/document/d/1q-PBeQELzT4pkgxB2ZOxGxwv6ynOixfzqzsFlCJ9jrw/edit

      You laugh at the beliefs of YECs and yet you are the one who believes that the stunning levels of integrated complexity we find in life, that our best computer engineers and programmers can only dream of imitating, happens all by undirected random processes. I would laugh at the insanity of your delusional belief, but it is too sad for me for I realize you actually are a human, and thus reflects very badly on me that a fellow human could be so delusional as to believe such tripe!

      Delete
    46. ba77: No oleq, you are the one making the extraordinary claim that biology is somehow immune to the effects of entropy. i.e. you actually have to show empirical evidence of Darwinian evolution!!!

      The sound of goal posts swooshing by!

      I have not made any claims, ba77. You have. You wrote that the second law of thermodynamics contradicts neo-Darwinism. It doesn't. No accepted formulation of the second law even mentions evolution. Therefore the burden is on you to establish the problem for neo-Darwinism.

      I don't have to establish anything until you make the connection between the 2nd law and neo-Darwinism. So far you haven't. You have pasted a bazillion irrelevant quotes, mentioned "genetic entropy" and black holes, but nothing whatsoever that links the 2nd law and neo-Darwinism. That's the breathtaking inanity we have come to expect from creationists.

      Delete
    47. No I wrote that the clear implications of the second law contradicts the second law. For you to hold that biology is somehow immune to the universal effects of entropy is a VERY extraordinary claim which demands extraordinary evidence (such as real time proof of Darwinian evolution!). This is not hard to understand and would stop ID dead in its tracks as far as rigorous empirical science is concerned. You simply have ZERO empirical evidence and are playing silly games because you know you can't defend from empirics! But such is the disconnect from reality we have come to expect from atheists!

      Since you will not provide proof, nor be honest with the proof provided to you, and will only play silly games just to avoid the clear implications of the second law, This is my last post to you on the subject. The last ad hominem insulting Christian theists is all yours.

      Delete
    48. "Clear implications" of the second law? Could you be a little more specific? What are they? Can you obtain them from the standard formulations of the 2nd law?

      Delete
    49. batspit77

      No I wrote that the clear implications of the second law contradicts the second law.


      Wow batspit77. Amazingly, you figured out a way to make your blithering incoherence be even more incoherent.

      Delete
    50. excuse me Thornton,

      I meant,,,

      No I wrote that the clear implications of the second law contradicts Darwinian evolution.

      Delete
    51. bornagain77: the clear implications of the second law contradicts Darwinian evolution.

      Then you shouldn't have any problems showing how the second law of thermodynamics contradicts neo-Darwinism.

      (Note to selves: Avoid trying to 'school' oleg in physics.)

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

    ReplyDelete
  5. Miller is a "hired hack". He "wuvs his wittle life wiff his doggies and farme liffie. He is willing to lie to any extent to "win the the argument". To me, this person is to be ejected from the discussion all together.

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  6. What is the ID explanation for the chromosome fusion evidence? Coincidence? Asking seriously.

    YOur clown, what the f is your explanation for how the chromosomes evolved by the supposed mechanisms thrust down our throats as fact. you dumb s t Good f g l d who the f are you anyway

    ReplyDelete
    Replies
    1. I take it you just experienced a new chromosome fusion event.

      Delete
    2. More likely a reversion back to the common ancestor.

      Delete
    3. Neither. Just extemely irritated at the high degree of illigitimate speculation and conjecture that plays such a fundemental role in the broad claims that "evolutionary scientists" make regarding living organisms and systems. Fully undisciplined imaginations run wild in the scheme, and it wouldn't necessarily be a problem if it didn't have such serious implications in society. If you have half a brain and are honest about it you can figure out something about those implications without me describing them for you.

      Delete
    4. bpragmatic, you don't seem to know much about evolutionary science.

      I suggest you learn something about it before you pass judgement on it.

      You need to have more than half a brain to understand this stuff, and thinking that all you need is half a brain is asking for trouble.

      It's not difficult, but it does require study, and a willingness to learn.

      Delete
    5. Liddle, I am not going to ask you what flavor of "evolution" we are talking about hear. We all know without going down another dozen rabbit trails.

      I know enough biology, biochemisty, genetic science etc. to recognize how incomplete your knowledge of living organisms and systems must be. Your arguments on this blog are trivial and actually specious much of the time. Actual empirical evidence in the sciences continue to demonstrate how bankrupt the traditional theory of evolution is.

      "and thinking that all you need is half a brain is asking for trouble." Seems to me having a full brain may cause problems at times as well. Apparently there are some reasonably intelligent people who are extremely gullible.

      Delete
  7. Excellent post Dr Hunter. It's very sad that Miller would stoop to such a level.

    ReplyDelete
    Replies
    1. Agreed, an excellent post, thank you Dr Hunter.

      Also thanks to ba77, as always, for the links.

      Delete
    2. Do you comprehend any of them, Jason? Can you summarize in your own words the scientific findings?

      Delete
  8. Cornelius, this must be either one of the most ignorant, or one of the most dishonest, posts of yours I have ever read. It will probably take several posts to deal with all the errors in it.

    You accuse Miller of “four key misrepresentations”:

    1. that the pseudogene has no function and is broken

    This is not a misrepresentation, as you must surely well know. A pseudogene by definition is a stretch of DNA that has a homologous coding gene (homologous in sequence and locus) but which does not code. In this case, the homologous coding gene codes for the beta part of haemoglobin, while the pseudogene does not, despite homologous sequences and locus. And we can readily see why: the start codon is missing, and there several other differences that would prevent the gene from being be expressed as a viable protein, even were the start codon to be reinstated. Phylogenetic analysis of this pseudogene suggest that the start codon was the first to be lost, which would have course have silenced it. Once a gene is silenced, there no conserving pressures, and so you would expect other mutations to creep in, and this is exactly what the phylogenetic analysis shows (Harris et al,1984). This is a scientific fact, and of course, like all scientific facts, does not come with 100% certainty, but that makes it no less of a fact, and it was established nearly three decades ago. Miller thus made no representation here.

    2. that the pseudogene DNA sequence has “errors” or “mistakes,”

    “Error” and “mistake” are lay terms, but perfectly clear ones. The pseudogene, unlike its coding homolog, has contains several features that prevent it from being expressed, including the missing stop codon, and other sequences that would prevent it from expressing a viable protein even should the start codon be repaired. Clearly these are not “errors” in the sense that a human being would make an “error” – but they are “errors” in two other important senses: they silence the gene, and they can be traced back to an original mutation in the stop codon that then ensured that further mutations (i.e. copying infidelities) would not be weeded out by selection. Miller thus made no representation here either.

    3. that there is no reason for broken genes aside from common descent

    There is certainly no other proposed reason, especially given the pattern of descent observable in the phylogenetics of the pseudogene. Why else would the pattern reveal a branched line of descent, starting with the missing stop codon, found in most primates, with accretions of various other variations, mapping neatly onto the observed morphological phylogeny of the primate clade? What other reason could explain this pattern? Apart from the whim of an Intelligent Designer, which could explain anything, and therefore nothing?

    4. that the evolutionary interpretation of such pseudogenes is objective science.
    Of course it is. It is independent evidence of a common ancestry for modern primates (independent of morphological phylogenies) and, moreover, fits perfectly with what we would expect to see, from evolutionary theory, given the non-disastrous silencing of a gene in a common ancestor, namely, gradual accretion of mutations that follow exactly the same phylogenetic pattern as that given by the morphological characters of the descendent populations. This is exactly what “objective science” is – the fitting of models to data, the making of new predictions, and the confirmation of those predictions by new data.

    It is hard for me to believe that, with your academic background, that you do not know all this.

    ReplyDelete
  9. CH: As was well known and documented when Miller and the ACLU lawyers devised Miller’s testimony, pseudogenes that had been investigated often exhibited functional roles, such as gene expression, gene regulation and generation of genetic diversity. Pseudogenes were found to be involved in gene conversion or recombination with functional genes. Pseudogenes sequences were found to be conserved with reduced nucleotide variability, excess synonymous over nonsynonymous nucleotide polymorphism, and other features that are expected in genes that have functional roles.

    Yes, of course. Pseudogenes are clearly good candidates for new function, provided their original silencing was not disastrous (sometimes the pseudogenes arise from gene duplication; after the gene has been duplicated, there is reduced conserving pressure on the two copies, as one can be silenced by a mutation without deleterious phenotypic effects).

    This is because they already have sequences that potentially code for useful bits of protein, and just as a badly-shuffled deck of cards will alter the odds of a good hand, a badly-shuffled (or scarcely shuffled) sequence of nucleotides has higher odds of becoming a good gene again, possibly with a new function, than a thoroughly shuffled.

    Again, Cornelius, you should know this; and, if you do, you surely have the smarts to realise that your argument makes no sense. It's as silly as the argument that because vestigial features may serve useful functions to the organism - including new functions - that they are not "vestigial".

    ReplyDelete
  10. CH: Miller’s pseudogene argument was just another example of a centuries-long history of religious mandates for evolution. Miller had been making such religious arguments for many years before Dover. He argued that life revealed features “that no engineer would stand for” so they must have evolved. That may be true, but such knowledge cannot come from objective science.

    As usual, Cornelius, you conflate a counter argument (in this case, an argument against Intelligent Design) for an argument (in this case for evolutionary theory).

    Evolutionary theory is not supported by the evidence that, if there were a designer, that designer can't have been very smart. It is supproted by the evidence for universal common descent, for the success of Darwinian mechanisms in producing adaptive evolution; by the observed mechanisms of inheritance and variance-generation; for the evidence for factors that result in speciation.

    All these things are perfectly consistent with a supernatural Intelligent Designer, as there is nothing that a supernatural Intelligent Designer cannot explain. However, these things are not consistent with the argument that there must have been a supernatural Intelligent Designer because no other inference makes sense, nor with the argument that the supernatural Intelligent Designer must have been omniscient, omnipotent and with human welfare at heart.

    But that is a problem for ID proponents and theologians, not for scientists. Scientists test hypotheses: Common Descent and evolutionary theory pass many tests. A supernatural Intelligent Designer is untestable unless we posit specific characteristics for that Designer, and when we do, it fails the test, as Miller correctly points out.

    ReplyDelete
  11. CH: Finally, Miller presented the chromosome fusion evidence as a “beautiful” confirmation of an evolutionary prediction.

    Which it is. One puzzle was why, if humans and chimps had a common ancestor, why chimps should have more chromosomes than we do. One hypothesis was that one pair of chromosomes in our common ancestors had fused, setting up a clear prediction. Which was confirmed. Beautiful indeed. The biological equivalent of finding the Higgs boson.

    What he didn’t explain to the court is that science is full of theories known to be false which yet make all kinds of confirmed predictions.

    Well, they are only "known to be false" when they make a prediction that is not confirmed. As long as a theory continues to make confirmed predictions, then that's as "true" as theories get in science.

    All theories are false, Cornelius. But some are less false than others. Science, as, again, you must know, is a continuous, iterative process of getting our models to fit ever more closely to our data. But they will never be a perfect fit. They are always, at best, incomplete, and so, in a very important sense, false.

    ReplyDelete
  12. As was well known and documented when Miller and the ACLU lawyers devised Miller’s testimony, pseudogenes that had been investigated often exhibited functional roles, such as gene expression, gene regulation and generation of genetic diversity. Pseudogenes were found to be involved in gene conversion or recombination with functional genes. Pseudogenes sequences were found to be conserved with reduced nucleotide variability, excess synonymous over nonsynonymous nucleotide polymorphism, and other features that are expected in genes that have functional roles.

    Any expert witness testifying on such a narrow topic would have been well aware of these well known results which were published by leading researchers in top tier scientific journals.


    Plaintiff's attorney: Objection! Irrelevant and immaterial. The attorney for the defense is citing facts that have nothing to do with the issue of common descent.

    The Court: Objection sustained.

    ReplyDelete
  13. Don't you need two fusion events, one in a male protohuman, and one in a female? Then they have to find each other and mate.

    ReplyDelete
    Replies
    1. No, although fertility will be reduced, for the original carrier, as only some combinations of gametes will be viable.

      However, once you have several carriers of at least one fused chromosome, the carriers will interbreed more successfully than carriers with non-carriers, and will increase the prevalence of carriers with both.


      So you actually have a nice mechanism speciation there, as you will have a subpopulation who will interbreed with each other more readily than with the main population, and will also tend to share a lot of alleles.

      Delete
    2. ... and comprehend it. (I know, I know, this is usually implied.)

      Delete
    3. BTW there's a nice Wiki article on Robertsonian translocations here.

      From the article:

      A Robertsonian translocation results when the long arms of two acrocentric chromosomes fuse at the centromere and the two short arms are lost. In this case, the long arms of chromosomes 13 and 14 have fused, but no genetic material was lost - this person is completely normal despite the translocation. Common Robertsonian translocations are confined to the acrocentric chromosomes 13, 14, 15, 21 and 22, because the short arms of these chromosomes encode for rRNA which is present in multiple copies.

      Most people with Robertsonian translocations have only 45 chromosomes in each of their cells, yet all essential genetic material is present, and they appear normal. Their children, however, may either be normal and carry the fusion chromosome (depending which chromosome is represented in the gamete), or they may inherit a missing or extra long arm of an acrocentric chromosome. Genetic counseling and genetic testing is offered to families that may be carriers of chromosomal translocations.

      Rarely, the same translocation may be present homozygously if heterozygous parents with the same Robertsonian translocation have children. The result may be viable offspring with 44 chromosomes[5].


      I guess the odds are that the individual with the original fused chromosome was male, and left a fair number of copies of viable 47-chromosome offspring around the population. If he was a particularly fit alpha male, that would make a lot of sense, as his 47 chromosome offspring would also inherit the good paternal genes, and tend to do well.

      When pairs of 47-bearers would mate, they would produce some homozygous (46 chromosome) offspring, and, in general, bearers of the fused chromosome would form more fertile couples with each other than with the rest of the population, enriching this interbreeding sub-population with fused chromosomes, and increasing the probability that they would go to fixation within that subpopulation, all bearers of genes from that original alpha male :)

      It's pretty neat.

      Delete
    4. Liddle:

      It's pretty neat.

      Not, it's not. It's pure unmitigated bovine excrement.

      I guess the odds are that the individual with the original fused chromosome was male, and left a fair number of copies of viable 47-chromosome offspring around the population.

      Where is the science in this pile of crap? Having 47 chromosome does not give an individual an evolutionary advantage over the rest of the population. The extant apes are proof that having 48 normal chromosomes works fine. Gorillas and chimps are powerful beasts.

      Delete
    5. Louis, you need to update your knowledge of evolutionary theory.

      A novel DNA feature does not have to be advantageous to go to fixation in a population.

      It can even neutral, or even slightly deleterious and still do so.

      Or it can be linked to a feature that does confer an advantage.

      Please do not dismiss perfectly good science as "bovine excrement" until you at least understand the science.

      Delete
    6. In any case, even if the fused chromosome had proved advantageous, your question amounts to "why are there still monkeys?"

      Delete
    7. Liddle:

      A novel DNA feature does not have to be advantageous to go to fixation in a population.

      Of course not. Otherwise it would falsify evolution. Right? Science by decree. We say crap is true, therefore it is.

      Please do not dismiss perfectly good science as "bovine excrement" until you at least understand the science.

      No thanks. I'm not particularly interested in gaining a thorough understanding of bovine excrement.

      Delete
    8. Louis Savain

      Where is the science in this pile of crap? Having 47 chromosome does not give an individual an evolutionary advantage over the rest of the population. The extant apes are proof that having 48 normal chromosomes works fine. Gorillas and chimps are powerful beasts.


      If 24 pairs of chromosomes works just fine, what is your explanation for why the Magic Designed gave humans only 23 pairs including the fused ones? I thought your "intelligent" Designers reused what worked and didn't reinvent the wheel. Why did we get the fused set?

      Have you ever looked at the chromosome count for equines? Horses have 64 chromosomes, donkeys have 62 chromosomes, while different zebra species have between 44 and 32 chromosomes. Why is that Louis?

      Do you have a supportable ID explanation for the observed widely different chromosome numbers?

      Delete
    9. Louis: Of course not. Otherwise it would falsify evolution. Right? Science by decree. We say crap is true, therefore it is.

      Yes, the discovery of the role of drift falsfied Darwin's theory. Evolutionary theory is being falsfied all the time. That's how science progresses.

      That is why evolutionary theory is so much vaster than it was in Darwin's day. You don't have to reinvent the wheel, Louis - decent hardworking scientists are way ahead of you, and have been, it seems, for several decades.

      Please do not dismiss perfectly good science as "bovine excrement" until you at least understand the science.

      No thanks. I'm not particularly interested in gaining a thorough understanding of bovine excrement.


      I think this is what is known as self-pwnage.

      Delete
  14. Louis: Of course not. Otherwise it would falsify evolution. Right? Science by decree. We say crap is true, therefore it is.

    You didn't understand what Liz was referring to. Genetic drift.

    No thanks. I'm not particularly interested in gaining a thorough understanding of bovine excrement.

    So declare mainstream science to be crap without understanding it. Ho hum.

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    Replies
    1. Genetic drift, my foot. There is no reason other than the usual speculative BS that the 48-chromosome humans disappeared from the earth.

      So declare mainstream science to be crap without understanding it. Ho hum.

      Mainstream science has always been full of crap. What else is new?

      Delete
    2. How well do you know mainstream science, Louis, to make such grand pronouncements? What's your scientific expertise?

      Delete
    3. A Masters in excrement, minor in bovine

      Delete