Home » Evolution, Genomics » Genome duplication and the limits of evolution

Genome duplication and the limits of evolution

“Genome Duplication Encourages Rapid Adaptation of Plants” (ScienceDaily, May 4, 2011)

While nearly all animals have two sets of chromosomes — one set inherited from the maternal parent and the other inherited from the paternal parent — many plants are polyploids, meaning they have four or more chromosome sets. “Some botanists have wondered if polyploids have novel features that allow them to survive environmental change or colonize new habitats,” says Assistant Professor Justin Ramsey. “But this idea had not been rigorously tested.”

Forcing duplication on wild plants (instead of the centuries old practice of forcing it on tame ones) produced quick results, as it does in tame ones:

Ramsey compared the performance of the transplanted yarrows and found that the hexaploid mutants had a 70 percent survival advantage over their tetraploid siblings. Because the tetraploid and hexaploid plants had a shared genetic background, the difference of survivorship was directly attributable to the number of chromosome sets rather than the DNA sequences contained on the chromosomes.

Those who think they have solved the abominable mystery of flowering plants tend to forget that the mega chrome types are just better adapted, not new species. Some sources think it best to wait 100 years to see if they dominate or just breed back into the common run (cf escaped pigs.)

  • Delicious
  • Facebook
  • Reddit
  • StumbleUpon
  • Twitter
  • RSS Feed

15 Responses to Genome duplication and the limits of evolution

  1. “Those who think they have solved the abominable mystery of flowering plants tend to forget that the mega chrome [sic] types are just better adapted, not new species.”

    Maybe a minor correction here-the polyploids are often reproductively isolated from the parental. If Yarrow 4X and 6X cross to make 5X the offspring aren’t very viable or fertile.

    Polyploids of many others species are totally reproductively isolated, and polyploidy is thought to account for a substantial percent of speciation events in plants.

    http://www.annualreviews.org/d.....t.34.1.401

  2. Here’s something I can’t figure out. There are I think 100 Trillion cells categorized into 600 types in the human I think. When a cell divides and the proteins begin to be assembled how do the machines inside the nucleus know which parts of the genome to consult in order to build the proper protein machine. Each of the 600 different cell types require different proteins. To me, at least, it looks like the machines that are using the DNA to build new proteins are simply conscious and they know what to do just like workers in a factory.

  3. Contrary to DrREC’s citation of ‘speciation’ from polyploidy, John Sanford, a expert in plant genetics, examines Polyploidy (Gene/Chromosome Duplication) fallacies in Appendix 4 of his book “Genetic Entropy and the mystery of the Genome”.

    “What about polyploidy plants? It has been claimed that since some plants are polyploidy (having double the normal chromosome numbers), this proves that duplication must be beneficial and must increase information. Polyploidy was my special area of study during my Ph.D. thesis. Interestingly, it makes a great deal of difference how a polyploid arises. If somatic (body) cells are treated with the chemical called colchicine, cell division is disrupted , resulting in chromosome doubling – but no new information arises. The plants that result are almost always very stunted, morphologically distorted, and generally sterile. The reason for this should be obvious – the plants must waste twice as much energy to make twice as much DNA, but with no new genetic information! The nucleus is also roughly twice as large, disrupting proper cell shape and cell size. In fact, the plants actually have less information than before, because a great deal of the information which controls gene regulation depends on gene dosage (copy number). Loss of regulatory control is loss of information. This is really the same reason why an extra chromosome causes Down’s Syndrome. Thousands of genes become improperly improperly regulated, because of extra genic copies.
    If somatic polyploidization is consistently deleterious, why are there any polyploidy plants at all – such as potatoes? The reason is that polyploidy can arise by a different process – which is called sexual polyploidization.This happens when a unreduced sperm unites with a unreduced egg. In this special case, all of the information within the two parents is combined into the offspring, and there can be a net gain of information within that single individual. But there is no more total information within the population. the information within the two parents was simply pooled. In such a case we are seeing pooling of information, but not any new information.”,,, “in some special cases, the extra level of gene backup within a polyploidy can outweigh the problems of disrupted gene regulation and reduced fertility – and so can result in a type of “net gain”. But such a “net gain” is more accurately described as a net reduction in the rate of degeneration.”
    John Sanford – Genetic Entropy & The Mystery of the Genome – pages 191-192 – Dr. John Sanford has been a Cornell University Professor for more that 25 years (being semi-retired since 1998). He received his Ph. D. from the University of Wisconsin in the area of plant breeding and plant genetics.,,, His most significant scientific contributions involved three inventions – the biolistic (“gene gun”) process, pathogen-derived resistance, and genetic immunization. Most of the transgenic crops grown in the world today were genetically engineered using the gene gun technology developed by John and his collaborators. (Due to such a stellar record in plant genetics, I take Dr. Sanford’s unmatched experimental experience of plants, strictly obeying the principle of Genetic Entropy, with never a violation, to be ‘state of the art’ for what we can expect for the polyploidy of plants).

  4. Bornagain-

    Somatic cell disruption is irrelevant to this scenario.

    ” The reason is that polyploidy can arise by a different process – which is called sexual polyploidization.”

    Indeed, this is what we’re taking about.

    “there can be a net gain of information within that single individual.”

    I thought that was a violation of the second law of thermodynamics. Oops.

    ” But there is no more total information within the population. ”

    Unless that individual is fertile. And with reproductive isolation, speciated.

    ” such a case we are seeing pooling of information, but not any new information. … But such a “net gain” is more accurately described as a net reduction in the rate of degeneration.”

    Except that this paper clearly demonstrates the hexaploid species GAIN function and GAIN fitness:

    “hexaploid mutants had a 70 percent survival advantage over their tetraploid siblings. Because the tetraploid and hexaploid plants had a shared genetic background, the difference of survivorship was directly attributable to the number of chromosome sets rather than the DNA sequences contained on the chromosomes.”

    So contrary to Sanford’s feelings that this is merely a gene ‘backup’ that might “outweigh the problems of disrupted gene regulation and reduced fertility,”
    there is clearly a gain in function and fitness.

  5. Excuse me DrREC, but to conclusively violate Genetic Entropy you would have to show a net gain in information above and beyond the information that was originally encoded within the optimal ‘parent’ species in the parent species native environment. The study, I believe, is derived from sub-species of a genus and reflects effects similar to the effects we witness from ‘compensatory mutations’ within ‘sub-optimal’ bacteria:

    Is Antibiotic Resistance evidence for evolution? – ‘The Fitness Test’ – video
    http://www.metacafe.com/watch/3995248

    DrREC, If all you require for ‘scientific proof’ for neo-Darwinian evolution is smoke and mirrors, then playing games with the variations found for sub-species of a parent kind is the way to go. But alas you have left scientific rigor and revealed that you treasure your bias more than truth in the process!

  6. BA77:

    Excuse me DrREC, but to conclusively violate Genetic Entropy you would have to show a net gain in information above and beyond the information that was originally encoded within the optimal ‘parent’ species in the parent species native environment.

    Genetic Entropy is a joke.

    DrREC:

    I thought that was a violation of the second law of thermodynamics.

    No. The more possible states there are the more “informative” a given state becomes.

    “Genetic entropy” is the ID’ists best friend, but not for the reasons they think.

    Is there a real connection between physical entropy and information? I think that’s the question we should be asking.

    Did the universe begin in a low entropy state and is now moving to a higher entropy state? What are the implications of that for any theory of information?

  7. Mung, if Genetic Entropy is a joke to you, then all you have to do to show me the humor in it is to show me a violoation of it by passing the fitness test I listed above!

  8. Mung as well, Walter Remine, whose work you have cited before, has signed off on the ‘joke’ of Genetic Entropy, and was instrumental in developing ‘Mendel’s Accountant’ with Dr. John Sanford, who is the author of “Genetic Entropy and The Mystery of The Genome”.

    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......aproof.pdf
    MENDEL’S ACCOUNTANT: J. SANFORD†, J. BAUMGARDNER‡, W. BREWER§, P. GIBSON¶, AND W. REMINE
    http://mendelsaccount.sourceforge.net
    http://www.scpe.org/vols/vol08/no2/SCPE_8_2_02.pdf

  9. Mung, if Genetic Entropy is a joke to you, then all you have to do to show me the humor in it is to show me a violoation of it by passing the fitness test I listed above!

    I saw a bunch of quote-mining. You didn’t list a fitness test, you provided a link to a page which contained a video and a bunch of links to other other pages.

    What, specifically, is a “the fitness test” and what does it have to do with “genetic entropy,” whatever that is.

    A common sense interpretation of “genetic entropy” is that the human genome (and the genomes of other species) is becoming more and more disordered over time. It is become more and more random, and contains less and less CSI.

    Yet at the same time we here at UD are touting “The Myth of Junk DNA.”

    You can’t have it both ways.

    I find it hilarious that alleged ID supporters on the one hand crow about how Darwinism predicts junk DNA and tout the notion of “genetic entropy” while failing to explain how “genetic entropy” doesn’t do the exact same thing (predict junk DNA). Care to address that?

    Genetic Entropy: The genome was created perfect by God, and it all goes down hill from there.

  10. Mung:

    Junk DNA is about non-coding regions by and large.

    The entropic challenge has in the key sense to do with the gradual accumulation of damage to functioning DNA through point mutations etc, embrittling the genome until it is breaking down. (In the race between the hoped for beneficial muts and the small effect damaging muts, the latter vastly outnumber the former and accumulate so net there should be a deterioration and breakdown.)

    Think about fancy dog pure-breeds and their even more fancy diseases.

    G

  11. mung;

    ‘What, specifically, is a “the fitness test” and what does it have to do with “genetic entropy,” whatever that is.(?)’

    Well Mung, basically Genetic Entropy means the blatantly obvious fact that unconscious material processes are completely impotent to generate any improvement on the works of Shakespeare, much less any improvement in the 100 million pages of functional prescriptive information in a simple bacterium!

    Notes:

    Thank Goodness the NCSE Is Wrong: Fitness Costs Are Important to Evolutionary Microbiology
    Excerpt: it (an antibiotic resistant bacterium) reproduces slower than it did before it was changed. This effect is widely recognized, and is called the fitness cost of antibiotic resistance. It is the existence of these costs and other examples of the limits of evolution that call into question the neo-Darwinian story of macroevolution.
    http://www.evolutionnews.org/2.....s_wro.html

    “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.
    http://behe.uncommondescent.co.....evolution/

    “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
    http://www.uncommondescent.com.....ent-363647

    “The manuals needed for building the entire space shuttle and all its components and all its support systems would be truly enormous! Yet the specified complexity (information) of even the simplest form of life – a bacterium – is arguably as great as that of the space shuttle.”
    J.C. Sanford – Geneticist – Genetic Entropy and the Mystery Of the Genome

    Systems biology: Untangling the protein web – July 2009
    Excerpt: Vidal thinks that technological improvements — especially in nanotechnology, to generate more data, and microscopy, to explore interaction inside cells, along with increased computer power — are required to push systems biology forward. “Combine all this and you can start to think that maybe some of the information flow can be captured,” he says. But when it comes to figuring out the best way to explore information flow in cells, Tyers jokes that it is like comparing different degrees of infinity. “The interesting point coming out of all these studies is how complex these systems are — the different feedback loops and how they cross-regulate each other and adapt to perturbations are only just becoming apparent,” he says. “The simple pathway models are a gross oversimplification of what is actually happening.”
    http://www.nature.com/nature/j.....0415a.html

    When faced with the staggering impossibilities of random material processes ever generating any functional information, Evolutionists would sometimes make the claim that an infinite amount of monkeys banging away on typewriters could produce the entire works of Shakespeare. Well someone humorously put that ‘hypothesis’ to the test:

    Monkey Theory Proven Wrong:
    Excerpt: A group of faculty and students in the university’s media program left a computer in the monkey enclosure at Paignton Zoo in southwest England, home to six Sulawesi crested macaques. Then, they waited. At first, said researcher Mike Phillips, “the lead male got a stone and started bashing the hell out of it. “Another thing they were interested in was in defecating and urinating all over the keyboard,” added Phillips, who runs the university’s Institute of Digital Arts and Technologies. Eventually, monkeys Elmo, Gum, Heather, Holly, Mistletoe and Rowan produced five pages of text, composed primarily of the letter S. Later, the letters A, J, L and M crept in — not quite literature.
    http://www.arn.org/docs2/news/.....051103.htm

    Evolution vs. Genetic Entropy – video
    http://www.metacafe.com/watch/4028086

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

    HGMD®: Now celebrating our 100,000 mutation milestone!
    http://www.biobase-internation.....mddatabase

    I really question their use of the word ‘celebrating’.

    ————

    Heather Williams – Hallelujah
    http://www.youtube.com/watch?v=81S-ZQsn8Kg

  12. OT: Checking out new speakers I got for computer with this song turned up loud:

    Skillet – Awake and Alive
    http://www.youtube.com/watch?v=2aJUnltwsqs

    Parental notice; NOT FOR THE FAINT OF HEART! :)

  13. “100 million pages of functional prescriptive information in a simple bacterium!”

    “a one-celled bacterium, e. coli, is estimated to contain the equivalent of 100 million pages of Encyclopedia Britannica”

    “Yet the specified complexity (information) of even the simplest form of life – a bacterium – is arguably as great as that of the space shuttle.”

    Hmm. That’s odd. E. coli only has 4,639,221 base pairs. Unless it takes 20-25 pages to encode a single base, I think your sources have committed some serious blunder.

    In fact, if you wish to see the entire E. coli genome, it take seconds to load in my browser:

    http://www.genome.wisc.edu/pub.....74v2-1.fas
    http://www.genome.wisc.edu/pub.....74v2-2.fas

    Kinda hard to take your sources seriously.

  14. Kinda hard to take your sources seriously.

    Seriously has nothing to do with it.

    I can swamp you with irrelevant BS.

    That’s all that matters.

  15. kf:
    Junk DNA is about non-coding regions by and large.
    Almost goes without saying.

    The entropic challenge has in the key sense to do with the gradual accumulation of damage to functioning DNA through point mutations etc

    So how does it take into account the non-coding regions of DNA, which by all accounts make up the vast majority of DNA?

Leave a Reply