We are all mutants

Measurement of mutation rate in humans by direct sequencing

http://www.eurekalert.org/pub_releases/2009-08/wtsi-waa082509.php


"Remarkably, the new research, published today in Current Biology, shows that these early estimates were spot on - in total, we all carry 100-200 new mutations in our DNA. This is equivalent to one mutation in each 15 to 30 million nucleotides. Fortunately, most of these are harmless and have no apparent effect on our health or appearance."

I'm not sure what you may be implying by these findings on mutations but one should bear in mind that most mutations in DNA of the nucleus are harmful to survival. Those you speak of are a product of the processes in the RNA outside the nucleus in the cytoplasm, and are the catalyst of real time input from the environmeent to transmit information to the DNA. This information would be the catalyst for more cell duplication that reflects for instance weight changes. Any mutations that would change the blueprint which gives us form and appearance would have to be mutations of the genes and that is what is harmful to survival. It would be helpful to have an understnading of atomic theory to grasp why mutations in truth are an anathema to an evolutionist. Just thought I would throw that in.

Exnihilo, that's totally incorrect. What's being referred to is, indeed, DNA mutation. Almost all mutations are neutral, being neither helpful nor harmful. Some are harmful and some confer survival/reproductive advantage, depending upon the environment. Under 'natural' conditions, natural selection tends to "weed out" the harmful mutations while preserving those that are beneficial.

Where do you get the idea that mutations are anathema to the evolutionist? Without mutations there would be no evolution, and no evolutionists.

Rede,
Good response.

Johnson, Laubengayer, DeLanney, Cole, write in their text "most mutations are harmful to survival", published by Holt, Rinehart, and Winston.

Yes, many mutations confer survival but those occur in the cytoplasm and pertain to protein synthesis. Those that are harmful occur in the nucleus of DNA and affect the helical DNA chain and cause malformation and death, which is not helpful to survival.

You are assuming evolution is a fact as a result of mutations. Darwin commented at the time he thought evolution was taking place but made sure it was known it was only an opinion. So far there is no scientific evidence to support it, just speculation.

That text is 40 years out of date.

Darwin believed that he had shown that evolution (descent with modification) had occurred and that he has a viable theory for how it had occurred (natural selection and sexual selection).

It is absurd to suggest that there is only speculation to support evolution. It's not just wrong, but ludicrous.

http://www.youtube.com/watch?v=i1fGkFuHIu0

There are known mutations in DNA that are not harmful. Do you have a current primary source that indicates that most DNA mutations are harmful?

The CCR5 mutation, for example, that provides HIV resistance is a beneficial mutation in DNA.

What exnihilo is saying appears to be quoted from the Encyclopaedia of Creation Science.

http://creationwiki.org/%28Talk.Origins%29_Most_mutations_are_harmful

That would explain his re-writing factual knowledge of simple, basic cellular biology in accordance with religious belief, and his ignorance of bountiful evidence of Darwinian evolution to the extent of denying any evidence whatsoever. There's nothing to be gained by attempting to feed a creationist with facts, nor by referring them to excellent books like:

'The Making of the Fittest: DNA and the ultimate forensic record of evolution', by Sean B. Carroll.

Meanwhile, creationist educators continue to try to remake the world in the image of their delusions.

Claim CB101: Most mutations are harmful, so the overall effect of mutations is harmful.

http://www.talkorigins.org/indexcc/CB/CB101.html

Incidentally, Holt, Rinehart and Winston is a publishing subsidiary (for grades 6–12) of Harcourt Education, based in...Austin, Texas.

The text I obtained and used for the quote was titled "Biology" by author's and publisher listed above,from the college I attended. Sorry for the inadvertant omission. What I wrote had no references or implications for creationism. The sequencing referred to and responded to has come from mitachondrial RNA in the cytoplasm. This was done because it was easier to sequence and study than nuclear DNA. So far there is no evidence there are significan mutations in the nulear DNA to alter the template of the dual helical DNA chain. Those that do occur relate to minor alterations of appearance such as eye and hair color.

I don't know how something "appears" to be a quote.

Here is a direct quote to me personally: "As a research fellow in molecular biology at one of our nation's most prominent universities I get to 'mingle' with some of the greatest scientist's in our nation, at work, seminar's,etc. I can say this much, the vast majority (95%) regard the hypothesis of evolution as laughable and within their inner circles is regarded with contempt. It is something of an in-house joke that so many people across the world have been taken in by this non-science and is illustrative of how 'science' can be used to manipulate thinking. The fact is that the general public is not very scientifically savvy and so tend to regard 'scientist's as something akin to 'gods' and if they say something it must be true, no matter how much it may strain common sense. My collegues in these sought after positions cannot publicly express their views at the moment because that would be 'biting the hand that feeds them' and they would not have jobs or research funds if they were to speak out against evolution. Some of the most fundamental scientific laws makes the foundations upon which evolution depends laughable." I have not advocated creationism nor dismissed evolution but there is ample reason to be suspicious of that has no basis in fact.

What?! Do you mean somebody said that as "a direct quote" to you personally?
Well that settles things. What an odd claim (95% regard the hypothesis...).
===

Aside from that inanity....

There's new info in 2009 about "accelerated mutation rates," but this below is all I could find quickly. I'll try to get the newer stuff--essentially a new mechanism for generating mutations--which is active only in humans and a few other higher primates.

but until then... I found this....
http://www.genetics.org/cgi/content/full/162/4/1825
Genetics, Vol. 162, 1825-1835, December 2002

Accelerated Protein Evolution and Origins of Human-Specific Features: FOXP2 as an Example

" I have not advocated creationism nor dismissed evolution but there is ample reason to be suspicious of that has no basis in fact.
"
No there isn't. Unsubstantiated quotes are not evidence. Not only are they not physical evidence; they aren't any kind of evidence.

I've met lots of people on the net who claim to be things they are not and claim to have credentials that they do not, in fact, have.
I know a few research molecular biologists - not many, but a few. All of them accept evolution. I'll name names: Dr. Harold Morowitz (molecular biophysics, Krasnow Institute, GMU), Dr. Thomas Schneider (NIH), Dr. Stuart Kauffman (inst for biocomplexity and information), Dr. Bonnie Bassler (Princeton). These are people I've met personally and whose bios you could easily confirm on the web - and read their articles and books. I do not know them well, but I've had brief conversations with each. There are many other researchers whose papers I've read. Also, the professional organizations for molecular biologists EXPLICITLY rejects creationism and accepts evolution:

http://en.wikipedia.org/wiki/List_of_scientific_societies_explicitly_rejecting_intelligent_design

The federation of scientists for experimental biology (FASEB)
which includes American Society for Biochemistry and Molecular Biology ( http://www.faseb.org/faseb/WhatIsFASEB.html ).

The group issued the following statement
http://www.fasebj.org/cgi/content/full/20/3/408
which explicitly supports the teaching of evolution and rejects the teaching of either creationism or "intelligent design" creationism.
"The Federation of American Societies for Experimental Biology (FASEB) has issued a statement supporting evolution and opposing the teaching of intelligent design and creationism in science classrooms. Supported by volumes of scientific evidence in numerous fields, evolution is among the most thoroughly tested theories in the biological sciences. The FASEB statement affirms that intelligent design and creationism are not science. "

Based on my personal acquaintances with molecular biologists and with the published statements of the leading societies of molecular biologists, I'm skeptical of your friend's claim.

In short, I don't see how unconfirmed assertions from anonymous people on the internet constitute a reason to be suspicious of evolution when can 1. find numerous molecular biologists who are actively engaged in evolution research and whose published works indicate a complete acceptance of evolution and 2. their own professional societies EXPLICITLY give strong support to evolution which seems EXTREMELY unlikely if 95% of the membership rejected evolution.

Hi, Samwik

Thanks for the link to the excellent article on PRM2 and FOXP2.

"We tackle this problem by comparing the rate of protein sequence evolution in the human lineage (since the human-chimpanzee split) with that in nonhuman mammals"

Although I don't see that a new mutation mechanism has been identified - the mechanism is still random substitution in the nucleotide sequence - it's no less an amazing achievement to identify two specific genes that suddenly proliferated (a >60 fold increase in FOXP2) somewhere between 40,000 and 100,000yrs ago, one essential to spermatogenesis and the other involved in speech and language development! No wonder humans spend so much time talking about sex

The speed of evolution and mutation must remain always balances in accordance to life conditions. Prokaryota still rely to horizontal gene transfer, simply because they can divide fast. Sexual reproduction is too mutagenic and energetically expensive for tiny organisms with fast paced live cycle (protozoa), so they using it only in under unfavorable conditions.

Large organisms can reproduce sexually, but sometimes tend to parthenogenesis under good life conditions: for example sharks are living in very stable conditions, so they don't evolve fast, they don't require mutations, so they're cancer resistant and hammerhead shark can reproduce asexually. An endometriosis and/or male associated infertility can be understood as an attempt for evolutionary adaptation of human organism to wealthy life conditions, where the sexual reproduction leads to unnecessary high mutagenity and cancer frequency in population. Good social conditions leads to unisex life style and male population will decline gradually in analogy to mixture of particles, which undergoes the gradual evaporation of smaller particles on behalf of large ones with lower social tension.

In AWT cambrian explosion was a result of analogous phase transition, a condensation of genes following from fast cooling. Around 530 million years ago Earth passed by so called "Snowball Earth" episode, i.e. by cryogenian period of strong cooling by the same way, like the Universe during inflation. During this a existing oceans were covered by thick layer of ice. This shock change of climate was followed by massive extinction, during which remaining organisms were forced to increase speed of their evolution and to exchange genes even in diaspora. The diaspora has lead into evolution of sexual reproduction, which is effective (and quite pleasant) method, how to increase gene mixing speed

I reiterate the blurb from the original post to this thread:

"Remarkably, the new research, published today in Current Biology, shows that these early estimates were spot on - in total, we all carry 100-200 new mutations in our DNA. This is equivalent to one mutation in each 15 to 30 million nucleotides. Fortunately, most of these are harmless and have no apparent effect on our health or appearance."

Again, for emphasis,
"... in total, we all carry 100-200 new mutations in our DNA."

A few points:
This was a recent study.
The article specifically refers to mutations in our DNA, not cytoplasm.
The implication is that by "our DNA," the author is referring to people like the author and the reader who are actually alive even though they contain these mutations.

Yes, but the mutations occur in mitachondrial DNA located in the cytoplasm, not in the nucleus where "replicating " DNA is located and mix through recombination. Any mutations that may be facilitors of a crossover process must be with replicating DNA. Most of the mutations of mitachondrial DNA are a response to environmental input and effect changes such as weight loss or gain, which effects cell duplication in real time. These mutations are prolific but have nothing to do with replication. This is a clear distinction between duplication and replication and cannot be construed as an evolutionary process. More of this discussed elsewhere.

The article says:

"An international team of 16 scientists today reports the first direct measurement of the general rate of genetic mutation at individual DNA letters in humans. The team sequenced the same piece of DNA - 10,000,000 or so letters or 'nucleotides' from the Y chromosome - from two men separated by 13 generations, and counted the number of differences. Among all these nucleotides, they found only four mutations."

Note it specifically says Y chromosome (that's the male stuff).

Mitochondrial DNA is matrilineal.

exnihilo: "Yes, but the mutations occur in mitachondrial DNA located in the cytoplasm, not in the nucleus..."

What's the problem, exnihilo? You do seem to have an axe to grind over this issue. If you read the article, you'll see that it discusses only chromosomal DNA, with no reference whatever to mtDNA. Mutations in the latter are more frequent...

"Despite many generations of separation, researchers found only 12 differences among all the DNA letters examined. The two Y chromosomes were still identical at 10,149,073 of the 10,149,085 letters examined. Of the 12 differences, eight had arisen in the cell lines used for the work. Only four were true mutations that had occurred naturally through the generations"

...but what's your point? Is it that you believe the researchers botched their project, and that all similar research results are false or falsified?

Yes, it was a direct quote. I had no reason to question its veracity. If you are questioning mine that is your perogative. I will close my contribution to this subject with the following and I beg your indulgence. It is based on thirty-five years of intense study of physical theory and related isues.

There are three legs claimed to support evolution and they are: natural selection, genetic drift, and mutations. None of these are direct evidence for evolution because none can provide evidence for a crossover process to accomomdate evolution. Crossover is a process that would facilitate changes from one species to another, and it must occur in nuclear DNA where the template of form for any species is located; that is, the DNA strand composed of genes and chromosomes. It is here any evidence forthcoming can satisfy an evolutionary process.

The accepted beginning for evolution is the single cell theory, all species evolved from a single cell containing DNA (there are cells that do not contain DNA) to one containing the DNA chain of a human many, many, thousands of genes and chromosomes later. The process of how all of this "building" can take place has never been explained, and it is the only way crossover from one species to another can take place.

Darwin started all of this with his observations over time of variations in traits and behavior of species and the results of his well-crafted conclusion he called natural selection, the differential survival of certain genotypes in a population through successive generations. He suggested a process of evolution was at hand but he noted it was only an opinion. He made no distinction between environmentally induced variations and inherited variations. It is now believed inherited variations contribute to evolution, and further claimed that mutations is the raw mateial accounting for it. I don't think there is any question of mutations contributing to traits because DNA research pretty much establishs it as fact. But to get to a reality of evolution from that is an entirely different matter, and requiires a better look at mutations and the dual helix of DNA.

This is the point mutations begin to fail as a reason for species evolution. Most mutations with nuclear DNA are deleterious in their effects and not helpful to survival (Biology 101}. To overcome this it has been proposed from a "thought" experiment suggesting once a population becomes large enough after a great deal of time selected mutations favorable to survival "could" occur. A thought experiment of this nature concluding something could occur is not acceptable, never mind in this scenario there is no reasoning of how a species might become large. All of it can be left-open to interpretation and can be judged at face-value, but thought experiments in this context is not evidence and the theory of evolution is laced with this kind of speculation. Natural selection provides a reasonable conclusion for "self-preservaton", but not evolution.

Recessive genes are behind mutations and inherited traits. These traits as we know them to be are such things as eye and hair color, countenance, and myriad other things we are familiar with. The dual helix of nuclear DNA has a specific form with various constituent parts that make it up. Each part has specific function and located at a specific site on the DNA strand, These specifics are important in understanding how mutations may or may not contribute to an evolutionary process. Gene recombination is the process of two genders contributing DNA and the genes match up in pairing on comparable sites of the DNA strands. Every gene is function specific in that it relates to a specific feature of a functioning organism. A recessive gene is one that becomes dominant and from mutation it alters a specific feature of the host. For example, eye color of an off-spring would be that of a dominant gene. The molecular formation of a gene for eye color assures that it will be a gene for eye color, and nothing else. There is a modest change of molecular formation from a recessive gene, initiated by mutation from recombination, but it will always basically be the same molecular structure of the combining genes. If that molecular struction in some wat is significantly changed it will never interact with its counterpart on the DNA strand. This is a result of disparity of covalence with particles at the atomic level by attraction and repulsion forces. It must maintain its original integrity of formation and this holds true for the entire DNA strand. This is why mutaions of replicating DNA is so inhospitalable. The only way a DNA strand can evolve from a single cell conaining a very tiny piece of DNA to one as large as a human's is through gene "creation" within a nucleus that "builds" all the rungs and tethered genes of the ladder of the representing DNA. New genes and chromosomes would have to be manufactured and migrate to,let's ssy, to one end of the ladder or the other beginning a new rung. There is some evidence of migratory genes but from one existent site to another existent site. Of course that means mutation by themselves cannot be the process for evolution.

Genetis drift? Genetic drif is the 'chance' fixation of a gene or group of genes in a small population. I believe the definition speaks for itself, but it involves mutant genes becoming dominant in a species. Again, a recessive gene is introduced through recombination and in successive generations by 'chance' only does it become dominant.
For all of the same resons as above genetic drift from mutations contributes to particular traits and appearances of a host and not to alterations of the DNA format. It isn' necessary to take it any farther.

One to itself or as a group, the main concepts as a support system for evolution cannot account for it. If a process can be shown to 'build' an evolving DNA chain it would be sufficient to validate he theory. There are hundreds of thousands of species on this planet and to say each evolved from a single cell branching off into hundreds of thousands of ways stretches even the smallest credulity. To pick out tiny snippets of an era and chosen similarties of species fitted selectively to appear as signs of evolution is misleading and should be treated as suspicious. There are good reasons for these similarities and they have nothing to with evolution, rather, they pertain to the very source and energy they arise from; a paradigm constructed by science. How mutation of genes that are site specific and function specific can build and/or expand a dual helix of DNA must be revealed to make evolution viable. A DNA template can be analogous to the blueprint of a house. One can build a house from a blueprint and over time make as many changes as they want altering its appearance, but it will always be a house and never anything else. Through mutations the outer appearance of an organism can change but it will always be that organism. In the case of living organisms sigificant changes are catalysts for asymmetry; malformation or fatal collapse. Plato was right, ideas and form is the reality, not appearances.

Finally. there are some who may be antagonistic of the above as a defense mechanism but it would be uncalled for. If there is a rational counter-argument I would be very pleased to hear of it. More references and links that do not address my thesis do not quality, unless they pertain to the specifics outlined here. Thanks for yourresponses.

exn: "Most mutations with nuclear DNA are deleterious in their effects and not helpful to survival (Biology 101}. "

It may have once been part of Biology 101 that most mutations are harmful, but subsequent, improved measures indicate that this is not true.

The article says "Remarkably, the new research, published today in Current Biology, shows that these early estimates were spot on - in total, we all carry 100-200 new mutations in our DNA."

As previously established this article refers to nuclear DNA, not mitochondrial DNA. EACH HUMAN CARRIES THAT MANY NEW MUTATIONS. That's a lot of mutations.

So pretty much, regardless of whether more or less of the do this or that, each person contains 100-200 new mutations.

Regardless of whether you personally believe that the existing mechanisms are sufficient, we can be quite certain that evolution has indeed occurred. ERV's are the smoking gun, but there are other convincing evidences.

Absolute proof is not a requirement of science. What would convince you of the validity of evolution isn't a necessary requirement to logically demonstrate evolution. Evolution has been established far beyond any reasonable doubt:

http://www.youtube.com/watch?v=i1fGkFuHIu0

You may have studied physical theory intensely for 35 years. I know a number of biologists, including the research molecular biologists whom I mentioned previously, most of whom have spent at least that long and have published ground-breaking research on the subject. They collectively have a very different take on the subject than you do.

I also disagree that Darwin was presenting natural selection as mere opinion. I've read Origin of Species 3 times, DoM, and his autobiography. He clearly was making what he felt was a very clear and compelling scientific that evolution does occur and how it occurs. That is not very relevant today, because the current theory is different and more complete than Darwin's and the evidence we have today is much stronger than what Darwin could have imagined.

Look, I accept the mutations of 100-200 mutations in our DNA but that in no way subsumes my theory. I accept mutations take place but there has to be a substantial chance they relate to a crossover process supporting evolution. Any notion they do is mere conjecture at this point and science has not improved on that prospect at all, especially since research is heavily
centered around mitachondrial DNA.

Do you realize that to get from a single cell to an organism such as ourselves requires hundreds of thousands of mutations that takes place on a site extant at any given time, and to effect crossover changes however minute a new gene must show up at a totally different location, by "building" new sites and functions adding to a DNA strand. You are effectively saying this takes place, but there just isn't any evidence to support that kind of process, no matter what anyone may think is happening.

I have not been denying evolution, I have simply iterated an opinion supporting my contention that is ample reason to be suspicious of it, and there is scientific and energy interaction processing that supports it. This support is much more inclusive and broad-based but it can't be outlined here. Sorry for that.

Self-preservation should not be confused with evolution. We do that by breathing or eating breakfast.

All I can say to your assertions is that your conclusions do not agree with those of most molecular biologists.

Watch the following video.
http://www.youtube.com/watch?v=uN3XZGgic4o

Then locate a gene that you think could not possibly have evolved and ask C0nc0rdance to test it.

Hiya rede....
Good to see you around.
Sorry this took so long, but....

I was trying to find a link to that information about a novel mutagenic pathway specific to humans (and a few other higher primates) involving mental and metabolic (see "The Second Brain") evolution.

Well, I ran across all sorts of interesting links while searching:
These first two are old standards that give a great overview of the wisdom behind evolution and genetics.

The rest sound great (I've seen the stem cell video--it's a winner--in case you've ever wondered how a cell knows its location in the body).

The last link
http://www.researchchannel.org/prog/displayevent.aspx?fID=572&rID=22219
is the one I was recalling--about a uniquely (almost) human mutagenic hotspot. It finally gets to the meat of the discussion after about 21 minutes (in a 58 minute talk), but the first 20 minutes are good background and orientation. At about 40 minutes it gets really interesting... and at about 50 minutes in, it will blow your mind!
Especially for you TFF!!!
===

I think the sciencedirect link (just above the last research-channel link) is research about the very topic being presented in the video.

a-CGH = array-based Comparative Genomic Hybridization

Enjoy!



***
http://www.researchchannel.org/prog/displayevent.aspx?rID=3229&fID=345
Endless Forms Most Beautiful
Description:
The Darwinian revolution was the first revolution in biology. University of Wisconsin--Madison's Sean B. Carroll traces the discovery of evolution through Charles Darwin's long voyage, many discoveries, and prodigious writings. Darwin introduced the concept of the 'fittest,' but how are the fittest made? The second revolution in biology was triggered by discoveries in genetics. Genetic variation, selection, and time combine to fuel the evolutionary process. The action of selection is now visible in DNA, both in preventing injurious changes and in favoring advantageous changes in traits.

http://www.researchchannel.org/prog/displayevent.aspx?rID=2513&fID=345
Making Genetic Networks Operate Robustly: Unintelligent Non-design Suffices
Description:
Mathematical computer models of two ancient and famous genetic networks act early in embryos of many different species to determine the body plan. Models revealed these networks to be astonishingly robust, despite their 'unintelligent design.' This examines the use of mathematical models to shed light on how biological, pattern-forming gene networks operate and how thoughtless, haphazard, non-design produces networks whose robustness seems inspired, begging the question what else unintelligent non-design might be capable of.
***


http://www.researchchannel.org/prog/displayevent.aspx?rID=19793&fID=345
Epigenetic Regulation of Genomic Imprinting
Description:
1. Become familiar with the concept of genomic imprinting, the genes that are subject to genomic imprinting and diseases that result from defects in imprinted genes.
2. Learn what the term epigenetics refers to and understand how epigenetic errors can lead to disease.
3. Gain an appreciation for the mechanism by which genes are imprinted.


http://www.researchchannel.org/prog/displayevent.aspx?rID=3218&fID=345
Human Genomics: A New Guide for Medicine
Description:
How different are two human beings from each other? Dr. Eric Lander explores human genetic variation, explaining how an understanding of small variations in DNA in individuals can help solve the mysteries of certain human diseases. Dr. Lander demonstrates an exciting new tool—the DNA microarray—that can be used to improve cancer diagnosis and treatment, and potentially increase our understanding of complex diseases.

http://www.researchchannel.org/prog/displayevent.aspx?rID=16091&fID=345
Understanding Embryonic Stem Cells
Description:
Embryonic stem cells, or ES cells, are cells that can be isolated from early embryos, before they differentiate into specific types of cells. Because stem cells have the potential to generate fresh, healthy cells of nearly any type, there is interest in exploring their use to treat and cure various diseases. The societal controversy regarding human ES cells relates primarily to their derivation from very early embryos. In addition, certain stem cell lines are developed using a cloning technique called somatic cell nuclear transfer, which can generate cells that are an exact genetic match to a patient.

--& look for part two at the Research Channel site....

===
http://www.sciencedirect.com/science?_ob...7a68bd0c1b9047f
"Non-coding RNAs, epigenetics and complexity"
[pay-per-view site] that sure sounds interesting!
===

http://www.researchchannel.org/prog/displayevent.aspx?rID=2741&fID=345
Computational Discovery of Genetic Regulatory Networks
Description:
With the draft sequences of many genomes in hand, the next frontier is understanding genetic regulatory networks that control cellular behavior and development. In our approach to discovering genetic regulatory networks we first learn about modules of genes and their interactions, and then refine this understanding into a model that describes the precise interaction of individual genes.

http://www.researchchannel.org/prog/displayevent.aspx?rID=11480&fID=345
Session 4: Interface of Engineering with Biology and Medicine, Part 1
Genetic Networks in Theory and Practice
&
Application of New Technologies to the Search for Genetic Determinants of Disease

http://www.researchchannel.org/prog/displayevent.aspx?rID=4492&fID=345
Genomic Study of Human Biology & Disease
Description:
The availability of the DNA sequence of the human genome has truly revolutionized biomedical research and is beginning to impact clinical care. Only about 5% of the 3 billion base pairs appear to be important, and finding and understanding these functional segments is one of the challenging problems that is being faced by biologists. Rick Myers, Ph.D., of the Stanford Human Genome Center examines how high-throughput genomic and genetic techniques are being applied towards identifying cis-acting transcriptional regulatory elements as well as the proteins that bind to them and control transcription.

http://www.researchchannel.org/prog/displayevent.aspx?rID=3230&fID=345
Selection in Action
Description:
The products of natural, and human, selection are all around us. Humans have transformed wild plants into useful crops by selective breeding and produced domesticated animals with sizes and shapes very different from their wild ancestors. Genetic crosses suggest that relatively few genetic changes are needed to dramatically transform the shape and structure of plants and animals. Natural selection in wild populations can also generate amazing diversity in a surprisingly short amount of time. David M. Kingsley, Ph.D. explains the genetic studies suggest that major evolutionary changes are controlled by a few key genes.

http://www.researchchannel.org/prog/displayevent.aspx?rID=3932&fID=345
Using Evolution to Explore the Human Genome
Description:
In this distinguished lecture, David Haussler talks about finding regions of the human genome that are not only under negative selection, but also are specifically evolving like protein-coding regions in genes. Haussler also investigates genetic innovations specific to primates and specific to humans. Given this as a base, and enough well-placed primate genomes to reconstruct intermediate states, scientists should eventually be able to document most of the genomic changes that occurred in the evolution of the human lineage from the mammalian ancestor over the last 80 million years.
***

http://www.sciencedirect.com/science?_ob...0f33dd3b8917a24
Duplication hotspots, rare genomic disorders, and common disease
The human genome is enriched in interspersed segmental duplications that sensitize approximately 10% of our genome to recurrent microdeletions and microduplications as a result of unequal crossing over. We review the recent discovery of recurrent rearrangements within these genomic hotspots and their association with both syndromic and nonsyndromic diseases. Studies of common complex genetic disease show that a subset of these recurrent events plays an important role in autism, schizophrenia, and epilepsy. The genomic hotspot model may provide a powerful approach for understanding the role of rare variants in common disease.

***
http://www.researchchannel.org/prog/displayevent.aspx?fID=572&rID=22219
The Changing Human Genome: Implications for Disease and Evolution
Description:
Dr. Evan Eichler, UW genome sciences professor and investigator with Howard Hughes Medical Institute, examines what current human genome research reveals about disease.
===

Wow, I just watched that last one again. Yep, it's almost all I recall (maybe there's a part two somewhere--possibly that "Session 4: Interface of Engineering ...Disease" link, or the one after that).

But this link above, with Dr. Evan Eichler, is a must see.
Well worth the time (or just cut to the last 10 minutes) to learn about the "unique" mechanism--an "architecture" leading to novel evolutionary capability in humans.

Good grief, Sam, you've been busy with that! I'll take a proper look at it all when I get a chance. Thanks a lot.

I did the searching, so I figured I'd share.

But it's only the last link (repeat of first link) that was the one I was talking about:
http://www.researchchannel.org/prog/displayevent.aspx?fID=572&rID=22219

...and just the last 10 minutes is the "unique" part.

Exnihilo

Needless to say, you're entitled to your honest opinion. To me - in the face of the vast wealth of evidence that you're choosing to ignore - your opinion counts for nothing. No disrespect, but that's my opinion. We'll have to leave it at that, I guess.

All of these points above explain why you have the view that you do.

I'd suggest the "Endless Forms..." video (see post at top of this page) to get the basics relating to your points, quoted above. Essentially one should think of genes as a tool box--each tool able to perform different functions at different times (in different forms), and able to take on new functions as opportunities present.

Your take on genetics is like looking at a dictionary and not comprehending how a great novel could be created.
Evolution rearranges words and phrases--even whole chapters at times--and is not just starting with a dictionary and trying to create "Pride & Prejudice" by changing single letters one-at-a-time.

Watch the video; you'll see:
http://www.researchchannel.org/prog/displayevent.aspx?rID=3229&fID=345
"....The second revolution in biology was triggered by discoveries in genetics. Genetic variation, selection, and time combine to fuel the evolutionary process. The action of selection is now visible in DNA, both in preventing injurious changes and in favoring advantageous changes in traits."

A gold mine. I doubt you'll see me on this forum for a while. thank you thank you thank you.

My fallible friend, I am just as fallible, and I can't pretend to know anything about homology. Thanks for the link. Look, I thought I made it clear that I am not dismissing evolution, on its surface it seems reasonable, but we are still dealing with conjecture and that isn't sufficient to substantiate it. Everything on the table is superficial and arbitrary and I merely pointed out many weaknesses. As far as intelligent design is concerned I have posed no opinion and my platform arises from an entirely different angle than all others. Please consider the following.

Biology is one tiny slice of physical theory and inherent in that related to our subject is that it doesn't take into account other contributing aspects. Whether a gene does this or that by itself does not satisfy anything. When genes interact with each other how they do it is all determined by disparate states of energy at the atomic level. How that process unfolds determines the state of genes at any given time. So if genes can mutate into something entirely different which is necessary for a crossover branching of species, its success depends on balancing these states of energy. Currently there is absolutely no consideration for this process at all in the conversation of evolution, and to get to a solution of design or not would have to be centered around the fundamentals of energy. Everything else is superficial.

Here's something else to consider. If evolution is correct and everything evolved by chance from a primordial cell, than there is something which should be evident in fossil recovery. In mutating from this to that over time a species would have to take on many forms of asymmetry. All fossils in recovery thus far display perfect symmetry. Fossils should reveal many states of asymmetry but that is not the case. If there is any it would be similar to any we see today in living organism's. This is quite glaring and it should tell those concerned why they should be suspicious of evolution. Not to say it is wrong, only that its viability has many problems. There has to be something more fundamental to support it than the arbitrary arguments posed today.

Studies in biophysics have confirmed the processes of duplication and mutation-- re: your comments about "Currently... no consideration for this process..."

But more importantly, when you say "Everything else is superficial" I think you should be more open minded. Are you saying no mechanisms for evolution, other than single nucleotide substitution, can possibly exist?

What about all the mechanisms (some of which address your good question about symmetry, from above) that are brought up in that Endless Forms... video:

http://www.researchchannel.org/prog/displayevent.aspx?rID=3229&fID=345

"There has to be something more fundamental to support it than the arbitrary arguments posed today." -exnihilo
I'd agree... if you changed that statement to refer to the arguments posed 30 years ago.

Your comments indicate that you are familiar with the conjectures posed 30 years ago, but not the current level of understanding. You're still talking about creating a great novel by switching around the letters in a dictionary.

...and you're not even considering epigenetics!

Please watch the video and check out the more current state of knowledge in basic genetics. The questions asked by the audience (students) are just as informative too.

If something is arbitrary than it is superficial. Advantages and changing traits are not the same as an evolving template of replicating DNA. It involves real-time phenomena extant at any particular time. The nuclear DNA does protect its integrity and most of that is signaled by RNA located in the cytoplasm, acting as a messenger for real-time phenomena. For example, the RNA would send a signal to duplicate cell formation to accomodate and reflect weight gain. This has a bearing on self-preservation but it does not suggest an evolutionary process. Anything else is conjecture.

While our knowledge has increased from thirty years ago, the conclusions made are still just as archaic. The inquiry should be concerned with asymmetry in fossil recovery but are there any studies really dealing with it? It is just too obvious to ignore. Why aren't there any fossils revealing asymmetry of any given species? They sould be prolific and gene mutation should not be confused with gene "formation", a process that would have to take place in order to get from a tiny piece of DNA in a singular cell to one as large as ours. That tiny piece of DNA would have to begin creating 'new" genes to add to its intrinsic gene pool for evolution to ensue. So, the question is how does gene mutation create new genes? Show that and the debate would probably end. Just like Darwin evolutionist's of today have to make a great leap of faith to say evolution is taking place.

I visited your links. They really have nothing new to add to the debate, and that is not being close-minded. It is just different lanquage saying the same thing. How in the world can Kingsley's study of vertebrates add anything to the debate?

Exnihilo says: "So, the question is how does gene mutation create new genes? Show that and the debate would probably end."

Anyone interested in the answer, go to this preview of the book 'Essential Cell Biology':

(Click on 'Contents' >> 'How Genes and Genomes Evolve', then scroll down to the next page, 295)

http://books.google.co.th/books?id=PKSeM...nes&f=false

See:
'Five Main Types of Genetic Change Contribute to Evolution'
'Genome Alterations Are Caused by Failures of the Normal Mechanisms for Copying and Maintaining DNA'
'DNA Duplications Give Rise to Families of Related Genes Within a Single Cell'

Exnihilo says: "Just like Darwin evolutionist's of today have to make a great leap of faith to say evolution is taking place."

See:
Long-Term Experimental Evolution in Escherichia coli. XII.
DNA Topology as a Key Target of Selection

http://www.genetics.org/cgi/reprint/169/2/523.pdf

http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=134600

redewenur__

Thanks for your comments. Your references including that of Feynman is noted. I'm going to give you a common sense response, it is up to you to give it credence or crdibility, but its logic is obvious. I don't have to visit your first reference because the sub-titles reveal all. Therefore, anything else would be redundant speculation for evolution from mutation to oooccur.

Unrelated pairings at comparable gene sites of recombining hosts begs the questions: how does a new gene manifest on a DNA strand? How does new and garbled ibformation representing transformation and branching, even modestly, for a foreign recombination? It would have to carry information totally unrelated to the recombining hosts. making it impossible to pair up in replication. Look, it doesn't do any good to focus on how a species might evolve, the inquiry should focus on how DNA evolves? That isn't a distinction without a difference. Mutations by themselves just isn't viable, and just as important the interactions taking place are all resolved at the molecular level, which isn't even part of the conversation.

Mutations as it stands today does not have a leg to stand regardless of what is "suggested" from current study. If you can provide to me a study that deals with my thesis, I would be eager to learn of it.

I'm sure you understand that forums are a soft target for crackpot pseudo-scientific theories, as users are rarely experts in the field under discussion (and it often takes an expert to demolish pseudo-science). But then, you maintain that you're not convinced by the experts, so we here are obviously wasting time.

Thirty-five years of intense study of physical theory and related issues, plus a radical theory opposing evolution? Go get your Nobel Prize, man.

I respect your reply but feel the strong antagonism. I'm sorry you felt it necessary. It would have been helpful to me if in some way could have responded to the questions asked, rather than open up an entirely different track. Thus far I have not proposed a "radical" theory nor seriously questioned the research on evolution, only its conclusions, based on what seems obvious. It should not be difficult to assimilate? I suggest before quoting Feynman one should examine the quote carefully. Your method of rebuttal does not fit this forum and venue.

Ex,

You made false statements about Darwin.
You were corrected. I have read OOS 3 times, DoM, and the autobiography. You were completely wrong and it would have been obvious if you had actually read Darwin.

You made false statements about the status of Evolution in the community of experts which you would not have made if you were aware of the the subject you were talking about. You used the argument from anonymous authority.
You were corrected with names of actual researchers and statements by professional organizations representing those whose opinions you attempted to convey yourself.

You made false statements about the relative ratios of bad mutations and supported it with a loose reference to a 40 year old text book.
You were corrected with more recent information, but if you had been studying this subject for 35 years you ought to have had a current source.

You made false statements about the article which you would not have made if you had even skimmed the article.
You were corrected.

You re-iterated false statements about the article which you would not have made if you had even skimmed the article.
You were once again corrected.

You then made other claims regarding the state of research and you buttress this claim by pointing out that you have "35 years of intense study of physical issues and related issues." Now this is clearly an attempt at argument from authority. Contrary to popular opinion, argument from authority can be perfectly legitimate in some cases - if the cited authority really is an actual authority.

Look, I've met LOTS of people who have "studied intensely" for long periods of time - years and even decades. Not all of these guys' studies are equal. There are a lot of non-anonymous experts out there who have put even more time than you have into the subject and much more dedicated. Now, given the track record of you have already achieved JUST IN THIS THREAD, I have to say, "No. I'm not going to accept you as an authority." Because "you say so" is not good enough.

You brought up another issue. Samwik appears to have addressed it, but you're not even going to watch the videos, because you assert without watching the vids that they don't address your objection. I have to tell you that your track record in this thread does not inspire confidence in your ability to ascertain facts from sources. In short, you're the one who should be paying close attention to what Feynman wrote.

The purpose of science is not to convince the people who think they have done their homework when they haven't or to convince denialists. Is it possible that the scientists who actually do research in the subject know something about it that you don't? That you're "research" may not be as air-tight as you suppose? You're of course free to respond to every post with "NUH UH" and proffer an objection that clearly indicates you haven't read what you claim to have read or that you haven't read anything current or that you refuse to examine the evidence that IS offered. Keep doing that. Science progresses and you just say, "NUH UH." At least the reason for your denialism appears clear at least to me: you just don't look at the evidence.

Your type of rebuttal doesn't deserve a response. Nevertheless, I will respond. Just once I would like someone like you to respond to one question I have posed on mutations without resorting to sarcasm. Your comments above says more about you than anyone else. Are you covering up your inability to answer the reasons for my skepticism of evolving mutations by your tactics? My questions are simple, reasonable, and have nothing to do with what you are trying to say or do. I don't question the research and its purpose, only some conclusions drawn that pertains to evolution, and that has not changed since the advent of genetics no matter what you are implying. The range of understanding of mutations has changed but not in context to some very basic questions. If there is evidence in context to those please convey them to me. Don't refer me to texts that can't provide any answers. You certainly seem to be threatened.

Exnihilo, TFF has taken the time to compose an entirely accurate and pertinent list of critical comments that I would have been well content to produce myself. Naturally, you find those comments unacceptable.

My method of rebuttal, also, doesn't suit you? But it's perfectly true, I'm sorely tempted to be facetious, seeing no further reason to attempt to humour you while you persist in taking yourself so seriously. Look, who are you to talk of evidence, for which you have such a blatant, wholesale disregard? By the garbage content of your posts, you've demonstrated that your logic has much in common with that of the conspiracy theorist and Bible literalist. For you, what counts is not scientific truth but maintenance of your irrational belief through selective ignorance of both evidence and established fact.

Just respond to the questions posed, not what bona fides someone may or may not have. I have not seen any comments addressing my questions, only those suggesting reading material. Please don't beg off in that manner. It seems to me your method is hiding behind an inability to deal with my questions. Those are not meant to impugn or deny anything or anyone and they don't, just opening up the discussion on other possibilities. You say there is evidence, just mention one in context that would add something to the debate. Instead you spew sarcasm and venom as a contribution. Sir/Ma'am, you should find some decorum or ask your mommy for your pacifier and become satiated with yourself. You deserved that.

I can see that you're upset, but when I say that you have a blatant disregard for the evidence, I'm not being venomous or sarcastic, I'm just stating the fact. When I say that you have posted garbage, that's not venom or sarcasm, it's fact. When I say that your logic has much in common with that of the conspiracy theorist and Bible literalist, I mean precisely that. I assure you, there's not a shred of venom or sarcasm therein.

Exn: "You say there is evidence, just mention one in context that would add something to the debate"

In the light of the above, that would be a total waste of time - and that's not venom or sarcasm, either. It's fact.

Deal with you questions?

You have been wrong at every message and you have been wrong in a way that suggests you are not interested to know the actual answers to your question, but are just throwing out what is called a bundle of sticks. That's not a mere claim - it's documented in this thread.

If your issues are real issues, then find another source besides yourself that says they're real issues.

It's not our job to do your homework for you.

Atomic theory is not as you claimed "anathema to evolution." You could have said, "I don't know the explanation for this" or "I'm not aware of what's been done here," but instead you make a clear statement for which you have not supplied any evidentiary support. The only support you have given is assertion; a dated, irrelevant reference; and a bogus claim by an anonymous "expert."

Deal with questions? I noticed you haven't answered any, nor how or where I have been wrong. I do know why atomic theory is an anathema to evolution and a mere statement does not require "proof" at this venue. I think wild statements abound as evidenced above and they don't qualify for ridicule and sarcasm. A "clear" statement can be a belief in something that is not in context to issues raised, namely mutating genes. I am not participating in this discussion to prove anything one way or another but to inject a different way of looking at the viability of genes and mutations that might be responsible for a radical alteration of genotyping in DNA. You seem to be bent on diminishing the messager and not the argument. If that is threatening to you than you have the problem.

I have answered a number of your false assertions, as ANYONE can tell who has followed this thread.

You wrote: 'I do know why atomic theory is an anathema to evolution and a mere statement does not require "proof" at this venue. '

You weren't asked for proof. You were asked for evidence. There's a difference. You supplied neither. You're saying that
"... we are still dealing with conjecture and that isn't sufficient to substantiate it (evolution)."

*We're* not dealing with conjecture - *you* are producing conjecture. You claim to have intensely studied "the physical theory and related issues," not a single sentence you have typed relates you have any significant understanding of the subject. Science isn't wrong just because you haven't done anything remotely resembling honest homework on the subject.

Sir, you are impossible and accomplish nothing. Does your credentials include being obnoxious?

What is obnoxious, and a cause of considerable concern to scientists, is the subversive attitude toward science - especially the science of evolution - of many people in the US; an attitude, founded on selective ignorance, that you have brought to bear in this thread. That is what is "anathema to evolutionists". For the sake of science education, neither you nor anyone else can be allowed to get away with promoting and propagating such nonsense. That, pal, is why you're being shot down.

You simply can't stand earnest criticism? Who are you to be a watchdog for the scientific community? I have contact with that august body and none of them have a problem with honest inquiry. Your arrogance does not fit a discussion forum of any venue but I'm sure you can't recognize why. You have preserved this thresd for your exclusive domain, I leave it to you and yours.

"You simply can't stand earnest criticism?"

I do not discern that your "criticism" was earnest. It was inept, uninformed, and persistently and egregiously mistaken.