On my latest blog, ThinkCreeps posted a comment quoting my statement that "we do not know why natural genetic engineering systems are as successful as they have been in generating useful evolutionary novelties in the history of life." Then he goes on to answer, "Yes we do - the good ones spread quickly through the population."
If only things were that simple! Good novelties just appear, as if by magic, and then spread due to their selective advantages. ThinkCreeps apparently shares a common illusion in evolutionary thinking that natural selection is all we need in the way of basic principles to understand the evolutionary process.
All scientific views of evolution by descent with modification envision two separate and essential steps in the establishment of living organisms with novel features:
In the absence of detailed information about the mechanisms of variation, heritable differences were widely assumed to arise randomly and accidentally. After Mendelism was rediscovered at the start of the 20th century, Mendelian segregations were added as variation modes in the neo-Darwinian "Modern Synthesis." Nonetheless, the sources of new segregating alleles (genetic differences) were still assumed to be stochastic accidents.
It was even claimed by some neo-Darwinians that evolution could be ascribed to changes in allele frequencies in populations due to natural selection acting on their fitness contributions. Many thinkers did not notice that this argument neglected the large number of cases where evolutionary differences were accompanied by other kinds of heritable change, such as alterations in chromosome structure or number.
With the advent of molecular genetics and DNA sequencing in the second half of the 20th century, it became possible to study the mechanisms of genome change in detail. It is commonly assumed that genome alterations account for the vast majority of heritable variation in living organisms. Other kinds of heritable changes are known and may also play an important role in evolution. Non-DNA changes include inheritance of self-templated cell structures and protein conformations, such as prions.
The results of the molecular studies are clear. Heritable changes can occur at the genetic level, through alterations in DNA sequences and in the structures of cell DNA molecules, and at the epigenetic level, through alterations in the way DNA is modified chemically and complexed with RNA and proteins in stable chromatin configurations.
Genetic and epigenetic changes result from the actions of cell biochemical activities, not from accidents. This is a critical fundamental discovery of molecular genetics.
There are many different activities that work directly on DNA and bring about genetic changes, ranging from single nucleotide substitutions to major restructuring of chromosomes. DNA modules can move from one place to another in the genome, RNA molecules can be reverse transcribed into DNA and inserted into the genome, and broken DNA molecules can be rejoined in novel combinations. The genome sequence record provides a rapidly growing mountain of evidence showing how important such non-random events have been in evolutionary history.
There are also many distinct activities that modify DNA and chromatin structures leading to heritable epigenetic changes. Our knowledge of these chromatin remodeling processes is younger than our acquaintance with DNA changes, and they do not leave the same kind of trace in the genome sequence record. But we do know that epigenetic changes have a profound influence on genome restructuring activities, and the same ecological challenges and stresses lead to high levels of both epigenetic and genetic variability.
Important take-home lessons from the molecular studies are:
To ignore all the above and look only at selection seems to me a gross omission. How could natural selection operate so that "the good ones spread in the population" if there were no positive variants in the first place? Where would they come from? That is why I am so confounded by Jerry Coyne's comment that he can explain natural genetic engineering by "garden variety natural selection." He's confusing baking the cake with eating it.
The outstanding issue, in my opinion, is: Where does functional creativity come into play to generate useful novelties? Darwin applied his uniformitarian, gradualist ideas to suggest that it was natural selection alone: "If it could be demonstrated that any complex organ existed, which could not possibly have been formed by numerous, successive, slight modifications, my theory would absolutely break down. But I can find out no such case" (Origin of Species, Chapter 6). However, we should note that Darwin modified his position in later editions to acknowledge "variations which seem to us in our ignorance to arise spontaneously. It appears that I formerly underrated the frequency and value of these latter forms of variation, as leading to permanent modifications of structure independently of natural selection" (Origin of Species, 6th edition, Chapter 15, p. 395, emphasis mine).
Now that we know how "spontaneous" variations arise, it is time to recognize that we cannot have selection without variation by natural genetic engineering and epigenetic modifications. To make further progress in our understanding, we need to investigate the respective roles of natural genetic engineering and natural selection in evolutionary innovation. Where, in fact, do "the good ones" really come from?
Bill Chameides: The Chemical Exposure that Keeps Going and Going and Going
http://www.stemedcoalition.org/
They will also find especially useful, the University of California, Berkeley's online educational resource on biological evolution, with this portion of its extensive website devoted to assisting teachers from K-12 grade levels:
http://evolution.berkeley.edu/evolibrary/teach/index.php
Other, more succinct, resources can be found at NCSE's website, especially here:
http://www.ncse.com/evolution
and here:
http://www.ncse.com/religion
I also highly recommend Brown University cell biologist Ken Miller's web page:
http://www.millerandlevine.com/km
Finally, last, but not least, this online resource devoted to Darwin's life and work is still quite appropriate, having been developed primarily by American Museum of Natural History invertebrate paleobiologist Niles Eldredge, curator of the Darwin exhibition, and noted historian of science David Kohn, highly regarded as a scholar devoted to Darwin's life and work, who was a key consultant to this exhibition:
http://www.amnh.org/exhibitions/darwin
Lemmingroom - give us more details on your teaching methods. There must be many biology teachers following this blog. Help them put into practice your methods. You remind me of Jamie Escalante, the math teacher in east Los Angeles who taught calculus to student who many thought incapable of learning such advanced material.
Perhaps the insights provided by Shapiro's concept of 'natural genetic engineering' can be of use to you in stimulating the natural curiosity that all young people have.
http://www.millerandlevine.com/km
Other effective teaching strategies are those currently used by elite science and mathematics-oriented secondary schools such as Fairfax County, Virginia's Thomas Jefferson High School of Science and Technology, and New York City's Bronx High School of Science (whose distinguished alumni include seven Nobel Prize laureate physicists), Stuyvesant High School and Brooklyn Technical High School. These teaching strategies are the ones that should be used to teach biology in American public and private secondary schools.
To change the perception of evolution as a "solved" problem is why I make the arguments I do on this blog. I plan to discuss some possible experiments for deepening our understanding of natural genetic engineering capabilities in future postings.
Please let me know if you think those arguments and suggestions are worth making."- Dr. Shapiro
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Im with you Dr. Shapiro, I think science needs to research just "how far mechanisms for activating and targeting natural genetic engineering functions can coordinate to produce more complex innovations prior to selection". It would be fascinating to know about some of your proposed experiments, However, I am astounded by the extreme resistance of your detractors to even consider venturing into this line of research. I would dare to say that they will attempt to do exactly the same as they do with the ID scientist and outright reject any of your possible experimentations out of hand, even before you begin.
Let their actions be a strong indication to you that you are on the right track!
We are discovering more and more bacterial and viral sequences in the genomes of complex organisms all the time. I have collected a whole bunch of references on this and other virus-related subjects at http://shapiro.bsd.uchicago.edu/ExtraRefs.Virosphere.shtml and under some of the headings at http://shapiro.bsd.uchicago.edu/ExtraRefs.NaturalGeneticEngineeringAndEvolutionaryGenomicInnovation.shtml .
Let me know if you need help with the bibliographies. I suggest browsing the titles of the articles and clicking on the links for articles that look interesting.
I forgot to mention that acquisition of information from viruses and from other organisms plays a major role in evolution. Here are some relevant examples from the bibliographies:
Bird, D. M. and H. Koltai (2000). "Plant Parasitic Nematodes: Habitats, Hormones, and Horizontally-Acquired Genes." J Plant Growth Regul 19(2): 183-194. http://www.ncbi.nlm.nih.gov/pubmed/11038227.
Acquisition of the ability to parasitize plants by receiving DNA information from other organisms.
Black, S. G., F. Arnaud, et al. (2010). "Endogenous retroviruses in trophoblast differentiation and placental development." Am J Reprod Immunol 64(4): 255-264. http://www.ncbi.nlm.nih.gov/pubmed/20528833.
Retroviruses in evolution of the placenta.
Boyer, M., N. Yutin, et al. (2009). "Giant Marseillevirus highlights the role of amoebae as a melting pot in emergence of chimeric microorganisms." Proc Natl Acad Sci U S A 106(51): 21848-21853. http://www.ncbi.nlm.nih.gov/pubmed/20007369.
Viruses mixing DNA from different kingdoms of life.
Buzdin, A., E. Kovalskaya-Alexandrova, et al. (2006). "At least 50% of human-specific HERV-K (HML-2) long terminal repeats serve in vivo as active promoters for host nonrepetitive DNA transcription." J Virol 80(21): 10752-10762. http://www.ncbi.nlm.nih.gov/pubmed/17041225.
Conley, A. B., J. Piriyapongsa, et al. (2008). "Retroviral promoters in the human genome." Bioinformatics 24(14): 1563-1567. http://www.ncbi.nlm.nih.gov/pubmed/18535086.
Viruses contributing to expression networks in our genomes.
1.Hereditary change is an active cell process rather than a passive series of accidents;
2.Hereditary changes affecting the whole genome can happen rapidly;
3.Biochemical processes that generate genetic and epigenetic variation are subject to control and targeting within the genome by cell regulatory networks; and
4.Cell change activities reflect the life-history experience of the organism and thus provide the basis for ecological feedback into evolutionary variation.
To ignore all the above and look only at selection seems to me a gross omission. How could natural selection operate so that "the good ones spread in the population" if there were no positive variants in the first place? Where would they come from? That is why I am so confounded by Jerry Coyne's comment that he can explain natural genetic engineering by "garden variety natural selection." He's confusing baking the cake with eating it." - Dr Shapiro
What else can Coyne do? Your evidence smashes the "Tow the Line" antiquated theories he promotes in his last published book. Too bad for his incompetence. Now he and others who continue to deny the obvious shortcomings of evolutionary theory and suppress the empircal evidence presented by Dr. Shapiro will one day have to come to grips that they put their self interest before science! History will remember and not be kind to them!
Perhaps the first religion Coyne needs to shut down is his own...
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Shapiro's statements do not eliminate the impact of mutations caused by known mechanisms such as gene doubling, transcription errors, meiosis errors, retroviruses, horizontal gene transfer, etc. Moreover, he is not eliminating the role of natural selection. Regardless of the source of a heritable trait, the viability of a trait IS determined by natural selection.
Shapiro is suggesting a supplemental understanding of the source of genetic change and not a wholesale replacement of evolution.
Viewing Shapiro's theory as a scientific basis for ID or a complete repudiation of evolution would be a dramatic misreading of what he has posted here as well as ignoring all of what he has said, including an unqualified rejection of ID.
Whether what Shapiro has proposed will replace the current understanding of evolution has yet to be seen.
Fortunately, after 18 years of that oppressing tension, I've developed teaching methods that allow me to present facts without ever using any of those terms, evolution, creation, or intelligent design. Students come to their own conclusions about survival, reproduction, and change. Since these lessons allow me to refer to taxonomy, natural selection, DNA, RNA, protein synthesis, enzymes, mutations, etc. without hitting that "evolution vs creation" nerve, they've survived all this time and I will continue to improve them in my next 18 years of teaching. No one is mis-informed (not knowingly, anyway), and the study of life continues without the threat of anyone being burned at the stake.
I've evolved as an educator :)
Mutations in viruses occur after they have infected cells. Of course mutations occur, but by cell biochemical actions, not by random accidents. Are you trying to say there is some difference between natural genetic engineering and mutation?
How and when mutations occur is critical to evolution, especially when the genome is undergoing major change. That is the point I am trying to make now that we understand something about the basic mechanisms of genome change (= mutation).
Adaptation is an active process. Since it's crucial to survival, it can't help but be conserved by natural selection!
>8-\
Some have made the conclusion as to 'success' with absolutely no frame of reference at all, what is fancied as handmade Swiss watches could just as easily be accidental sundials. I find myself in 'ThinkCreeps' camp on this.
Far too often, our current rigid scientific method paradigm, particularly endorsed by physicists lacks humility, which stifles imagination allowing us to acknowledge and more fully explore what is more often than not unthinkable, yet, reality; demonstrated by biological observation described. The final question proposed by Dr. Shapiro is perfect example why we should try harder to keep an open mind.
Another interesting statement, "Genetic and epigenetic changes result from the actions of cell biochemical activities, not from accidents."...suggests potential intelligent organization and action.
If true, and why not believe it, then two questions arise: Can we eventually learn to influence biological outcomes as well? And back to Dr. Shapiro's question, what influence is driving this organizational influence currently?
Personally, I'm inclined to imagine influence from high energy subatomic QM fluctuations just as I'm inclined to believe consciousness is connected as well. Time (no pun intended) will tell, friend.
As for the points made by the author you know that I'm not in any place credential wise to argue one way or the other, my point was to put the discussion into context, that what we see as wondrous or too complicated may simply be not true because we have no comparisons with other 'natures'.
As for keeping an open mind, I have no choice but to do so.....because it's my 'nature' ;-)
You hit the nail on the head! The question now is: How far can they leap in a single bound?
The DNA sequence record documents sudden genome changes accompanying major evolutionary transitions. Successive genome doublings at the origins of vertebrates and then jawed vertebrates are cases in point.
The DNA sequence record also provides evidence of bursts of adaptive changes in the evolutionary histories of many taxa (e.g. http://www.ncbi.nlm.nih.gov/pubmed?term=21852499). A number of these changes are associated with mini-saltations, such as the movement of mobile genetic elements to new locations in the genome (http://www.huffingtonpost.com/james-a-shapiro/more-evidence-on-the-real_b_1158228.html).
The question is whether we can reproduce these bursts in real time. We can already do this on a small scale for individual traits. Now we need to look at more complex adaptations. Accomplishing such complex saltations would transform molecular macro-evolution from an inferential historical subject to a true experimental science.
Why would they come from anywhere different than the "bad ones"? Isn't the only difference from the "good ones" and the "bad ones" is that "good ones" give a survival advantage and so have a higher chance of propagating? Isnt't this what is usually called natural selection?
As a non-biologist I remain mystified by these posts. I wish the author would spell out clearly the point he is trying to make. I get the impression that some form of intelligent design might be hinted at but it's never clearly spelled out, or if it is, it's with so much jargon as to be obfuscated to the uninitiated. I'm impressed with the author's willingness to engage with his critics but I'm not seeing illumination from it.
If this is, in fact, just a discussion on the technical details of how mutations arise, that's fine, as far as it goes, but that's not the sense I'm getting from it.
Shapiro is addressing the technical details of how useful mutations arise; he is saying they do not happen by accident and they are often sudden not gradual; he terms the mechanisms that drive this "Natural Genetic Engineering." These mechanisms have been persistently ignored, and swept under the rug by the Jerry Coynes of the world. They don't want you to think about any of this. They want you to think Natural Selection explains almost everything.
Natural Selection is just a delete key. As such it's really not all that interesting. The actual mechanisms of mutation are endlessly fascinating and we have much to learn by studying them.
I think I'm finally understanding what you folks are driving at but it seems to me like an emergent pattern producing the illusion of cognitive action. Just as, in mainstream evolution, a species might appear to be responding to its environment when its individuals are just undergoing random mutation and selective culling, an organism could give the appearance of responding to stresses when its components are acting much like individuals in mainstream evolution.
I guess I'm saying that this could just be a level of abstraction thing. I still don't see any room for a cognnitive "ghost" to be making decisions about mutations. All that said, I'm not a biologist so I'm only talking with a layman's competence here.
"Natural selection is a mechanism by which populations adapt and evolve. In its essence, it is a simple statement about rates of reproduction and mortality: those individual organisms who happen to be best suited to an environment survive and reproduce most successfully, producing many similarly well-adapted descendants. After numerous such breeding cycles, the better-adapted dominate. Nature has filtered out poorly suited individuals and the population has evolved."
"V.I.S.T.A."
"Natural selection is a simple mechanism that causes populations of living things to change over time. In fact, it is so simple that it can be broken down into five basic steps, abbreviated here as V.I.S.T.A.: Variation, Inheritance, Selection, Time and Adaptation."
You and others can look here for more information:
http://www.amnh.org/exhibitions/darwin/evolution/work.php
We know today that cells possess specific biochemical functions to change their DNA. These functions respond to various challenges and stresses experienced by cells and their host organisms. Their actions can be targeted within the genome.
The DNA record shows us that this kind of self-mediated genome change, which I call "natural genetic engineering," has produced many adaptive elements in our genome (e.g. http://www.huffingtonpost.com/james-a-shapiro/more-evidence-on-the-real_b_1158228.html).
Now that we know about natural genetic engineering, we can no longer confuse ourselves by thinking that variation is a random process. Thus, it is necessary to explore how far cell capabilities extend in crafting useful genome novelties.
The creative aspects of evolution have a new home in natural genetic engineering, not in natural selection. Genome sequences document this for new proteins and new regulatory sites.
But we do not know how far mechanisms for activating and targeting natural genetic engineering functions can coordinate to produce more complex innovations prior to selection. The genome record suggests more complex innovations involved sudden changes like genome doubling.
To change the perception of evolution as a "solved" problem is why I make the arguments I do on this blog. I plan to discuss some possible experiments for deepening our understanding of natural genetic engineering capabilities in future postings.
Please let me know if you think those arguments and suggestions are worth making.
I tend to agree with Dr John Sanford (Geneticists and inventor of the GeneGun) when he said .
“The bottom line is that the primary axiom [of Darwinian/Macro evolution] is categorically false,
you can't create information with misspellings, not even if you use natural selection.”
The evolution battle is often MISrepresented as science against religion - this is baloney.
The real battle is between science and Darwinism.
The scientific evidence supporting Darwinian/Macro evolution is woeful, when it is scrutinised critically (as the scientific method demands) IT CRUMBLES!!!.
It would be helpful if there was a clear and consistent definition of "Evolution". Evolution is a vague word.
Micro evolution is minor changes within a species, this is real and observable and uncontested.
The conflict pertains to Darwinian/Macro evolution which asserts that:
1) All living things had a common ancestor. This implies that your great….. great grandfather was a self replicating molecule.
2) The observable world has come into existence by totally natural, unguided processes and specifically WITHOUT the involvement of an intelligent designer.
The vague and changing definition is poor science and a thinly disguised strategy to make it easier to defend and propagate.
Such a claim, however, is entirely false. The theory of evolution explains the process by which existing biodiversity emerged from common ancestry. This process does not and cannot address the means by which the entirety of "the observable world" came to exist and thus it cannot claim that an "intelligent designer", as vague and undefined as the concept may be, was not involved during some step of the process.
Your statement demonstrates a fundamental lack of understanding of the subject of evolution. In so doing, you have demonstrated that you cannot credibly discuss the theory, and thus your objections to it are, at present, without merit.
Are we reading different text books or something?
Richard Dawkins, the eminent spokesman for evolution would definitely agree with my assertions about the process being unguided.
Darwin, also has no place for God in his book "On the Origin of Species"
Can you please clarify your position.
Again, thank you.
1) Me asking questions that, like you said, were "quite reasonable" and what I got was Darwinists ramming their dogma down my throat, and I was supposed to accept their unsatisfactory answers because "No credible scientist believes otherwise!" Methinks they doth protest too much.
2) At the same time I was never comfortable dismissing common descent. I was at odds with many creationistst/IDers, who felt evolution was an insult to their humanity. If evolution was true, it would be a very elegant way of harmonizing everything in biology and I saw evolution itself as an impressive engineering achievement.
In 2005 someone sent a link to Shapiro's papers and I was hooked. I came to understand that what Shapiro talks about has generally been understood for decades, but greatly downplayed by Darwinists, not taught to most biology students until Sophomore or Junior year, after they've completely swallowed the philosophical vacuity of "randomness + natural selection explains everything."
I'm open to supernatural explanations and I embrace the supernatural as an ultimate explanation. But I admire and embrace the rigors of methodological naturalism. So if you're ready to digest some challenging material, Shapiro's book has more real content per page than any other biology book I know.
(Note -- this reply is in two parts, since the comment section doesn't appear to allow comments over a certain length.)
Part One:
I did a massive study of evolution back in the '70s when my wife of the time, who'd been raised a Jehovah's Witness, challenged me to answer her arguments with something other than stock phrases that came from a high school text book. So I started digging into the original material (Simpson, Dobzhansky and a host of others). These proved unsatisfactory, since they tended to make pronouncements rather than reasoned arguments (not all the time, but enough that it bothered me -- and I was searching for the definitive proof that would silence my wife's irrational belief in Creationism). After than I went to the museum's library (Royal Ontario Museum) and began looking over the field work of the actual archaeologists. This took place over the course of about five years.
Eventually we were divorced, and I put my evolution research behind me, but would pick it up again every so often. There was a period during the early to mid '90s in which I saw several articles in the main stream media reporting on biologists openly stating that there were problems with the theory as it stood, but they quickly disappeared, and from then on it was business as usual.
(Cont.)
Mutations are rare -- that's why we tend to look like our great-great-great grandparents in basic form. Of the mutations that do occur, very, very few are advantageous (I'm not sure that any have yet been observed in a laboratory setting, but I may be wrong). Given this, we have two options.
In the first, a species stays the same for eons and eons, with the rare disadvantageous mutations being weeded out, and the even rarer advantageous mutations slowly being spread throughout the future generations. In the second, we allow for mutations to be numerous enough that the occasional advantageous ones have the opportunity to spread and through various stages resulting in a new species.
The problem with the first is that change would come so slowly that even a billion years is inadequate to result in the varieties of life we see on Earth. The problem with the second is that the number of bad mutations would quite rapidly wipe out the species.
The question isn't around natural selection -- it's around the remarkably fortuitous number of positive mutations that have occurred to produce the teaming life around us.