This New Paper on How Innovations Evolved Raises More Problems Than it Solves

_{Cornelius Hunter

July 16, 2013

Intelligent Design}

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It was not news this week when evolutionist Andreas Wagnerexplained that “we know very little about how they [evolutionary innovations] originate.” The origin of evolutionary innovations is largely unexplained and that gap is well known. No one would deny this. Even Wagner’s own press release begins with the same admission: “Exactly how new traits emerge is a question that has long puzzled evolutionary biologists.” But this admission, while uncontroversial, is not well advertised. It is not typically found in textbooks or popular books. Evolutionists do not often discuss this shortcoming in their class lectures or public talks. For this shortcoming is rather embarrassing. In order to be taken seriously evolution must be able to explain how life’s various and incredible innovations arose, and it hasn’t been able to do that. This raises two interesting tensions for evolutionists. Read more

Comments

Thanks Jerry very informative.

However this research does show that pointing the finger at secularism as the cause of social ills is probably not justified.
Actually the research points a very direct finger at secularism, the sexual revolution, the Great Society and the rise of the atheistic left and their culture of tolerance as responsible for the underclass. Charles Murray's book, Losing Ground, was responsible for Welfare Reform. His research showed not only did the government programs not help but they actually harmed. Along with this came an attitude that the underclass had no responsibility to work their way out of poverty. They were owed by the rest of society and this witches brew created a learned helplessness in a large section of our society where they became unable to do anything to help themselves. Over the years this change in attitude to not work oneself out of problems has migrated to other groups. All fed by a culture of tolerance as new self destructive cultures were created and tolerated. Below is the link for Losing Ground: American Social Policy, 1950-1980. Murray is hated by the secular left because he has exposed just what harm they have done. It is amazing that the Zuckerman article links atheism directly with these policies that caused all this harm. Zuckerman is very proud of his article but he fails to tell the whole story. Maybe he doesn't realize the connections but they are there to easily see. http://www.amazon.com/Losing-Ground-American-1950-1980-Anniversary/dp/0465042333/ref=sr_1_8?s=books&ie=UTF8&qid=1374195415&sr=1-8 Interesting is that Amazon doesn't list the Kindle edition. I have a Kindle copy.jerry_{July 18, 2013
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OT: Berlinski is back on Darwin's Doubt A One Man Clade - David Berlinski July 18, 2013 http://www.evolutionnews.org/2013/07/a_one_man_clade074601.htmlbornagain77_{July 18, 2013
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Thanks Jerry very informative.bornagain77_{July 18, 2013
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I don’t personally believe secularists are more moral etc. than religious people. However this research does show that pointing the finger at secularism as the cause of social ills is probably not justified.
I am sure a lot of the statistics that were quoted in the study you referenced are true but they may be cherry picked in such a way that does not present a true picture of the dynamics of the last 50 years. What the statistics may not be revealing is that the secular ones are children of religious people but also the inheritors of an incredible economic expansion that has affected certain groups much more positively than others. The United States has a large underclass that is extremely dysfunctional and this underclass is most probably the creation of a secular/elites mindset. Charles Murray wrote what I believe is the most important book of the last ten years and it will be ignored by the elites because it does not paint a pretty picture in the US for a large sub population which is where most of the problems lie that Zuckerman almost proudly points out. The book is
Coming Apart: The State of White America, 1960-2010
http://www.amazon.com/Coming-Apart-State-America-1960-2010/dp/030745343X The United States is separating in to social classes that did not exist before and it has been a gradual process since the early 1960's. Other countries are seeing similar things but the United States has probably one of the most heterogenous populations in the world. These social classes are based on education, intelligence and income which all tend to highly correlate. The underclasses are getting bigger and it is within some large sections of these underclasses that the identity of religion is probably highest. Not all the underclasses are religious because in the white underclass that is quickly growing has almost completely abandoned religion. There is no cause between the identity with religion and the poverty they find themselves in. I say that because the so called seculars are children of religious people and when they inherited the intelligence, income and education opportunities from their religious parents, a lot of them abandoned the religious tendencies of their parents. So a lack of religion is not the cause of their circumstances and a lot of their attitudes. And it is too early to tell what the lack of religion will do to the secularists or elites. Such a process will take decades to play out especially as the underclass grows and the secularists dwindle in size. I won't go on with this topic because it is not really the purview of this site. But if one is trying to associate atheism with positive attitudes on certain topics it is misplaced for a couple reasons. One is that the good fortune of the atheism can be attributed to a society that was built by religious people and secondly, the attitudes of the elites can be directly associated with the problems of the underclasses. Myron Magnet wrote a book about this showing that the so called tolerance of the elites is a cause of the lack of self discipline in the less intelligent and less educated.
The Dream and the Nightmare: The Sixties' Legacy to the Underclass
http://www.amazon.com/Dream-Nightmare-Sixties-Legacy-Underclass/dp/1893554023/ref=sr_1_2?s=books&ie=UTF8&qid=1374149267&sr=1-2jerry_{July 18, 2013
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Of related note: It is interesting to note that materialism/atheism leads to the epistemological failure of of man's noetic experience: The Atheist’s Guide to Intellectual Suicide – video https://vimeo.com/60437420 Should You Trust the Monkey Mind? - Joe Carter Excerpt: Evolutionary naturalism assumes that our noetic equipment developed as it did because it had some survival value or reproductive advantage. Unguided evolution does not select for belief except insofar as the belief improves the chances of survival. The truth of a belief is irrelevant, as long as it produces an evolutionary advantage. This equipment could have developed at least four different kinds of belief that are compatible with evolutionary naturalism, none of which necessarily produce true and trustworthy cognitive faculties. http://www.firstthings.com/onthesquare/2010/09/should-you-trust-the-monkey-mind Scientific Peer Review is in Trouble: From Medical Science to Darwinism - Mike Keas - October 10, 2012 Excerpt: Survival is all that matters on evolutionary naturalism. Our evolving brains are more likely to give us useful fictions that promote survival rather than the truth about reality. Thus evolutionary naturalism undermines all rationality (including confidence in science itself). Renown philosopher Alvin Plantinga has argued against naturalism in this way (summary of that argument is linked on the site:). Or, if your short on time and patience to grasp Plantinga's nuanced argument, see if you can digest this thought from evolutionary cognitive psychologist Steve Pinker, who baldly states: "Our brains are shaped for fitness, not for truth; sometimes the truth is adaptive, sometimes it is not." Steven Pinker, evolutionary cognitive psychologist, How the Mind Works (W.W. Norton, 1997), p. 305. http://blogs.christianpost.com/science-and-faith/scientific-peer-review-is-in-trouble-from-medical-science-to-darwinism-12421/ Materialism/Atheism simply dissolves into absurdity when pushed to extremes and certainly offers no guarantee to us for believing that our perceptions and reasoning within science are trustworthy in the first place: BRUCE GORDON: Hawking's irrational arguments - October 2010 Excerpt: What is worse, multiplying without limit the opportunities for any event to happen in the context of a multiverse - where it is alleged that anything can spontaneously jump into existence without cause - produces a situation in which no absurdity is beyond the pale. For instance, we find multiverse cosmologists debating the "Boltzmann Brain" problem: In the most "reasonable" models for a multiverse, it is immeasurably more likely that our consciousness is associated with a brain that has spontaneously fluctuated into existence in the quantum vacuum than it is that we have parents and exist in an orderly universe with a 13.7 billion-year history. This is absurd. The multiverse hypothesis is therefore falsified because it renders false what we know to be true about ourselves. Clearly, embracing the multiverse idea entails a nihilistic irrationality that destroys the very possibility of science. http://www.washingtontimes.com/news/2010/oct/1/hawking-irrational-arguments/ I strongly suggest watching Dr. Craig’s presentation, that I have linked, to get a full feel for just how insane the metaphysical naturalist’s position actually is. Is Metaphysical Naturalism Viable? - William Lane Craig - video http://www.youtube.com/watch?v=HzS_CQnmoLQ But perhaps the most direct proof that atheism/materialism is false is that atheists themselves don't live as if their worldview was true: The Heretic - Who is Thomas Nagel and why are so many of his fellow academics condemning him? - March 25, 2013 Excerpt:,,,Fortunately, materialism is never translated into life as it’s lived. As colleagues and friends, husbands and mothers, wives and fathers, sons and daughters, materialists never put their money where their mouth is. Nobody thinks his daughter is just molecules in motion and nothing but; nobody thinks the Holocaust was evil, but only in a relative, provisional sense. A materialist who lived his life according to his professed convictions—understanding himself to have no moral agency at all, seeing his friends and enemies and family as genetically determined robots—wouldn’t just be a materialist: He’d be a psychopath. http://www.weeklystandard.com/articles/heretic_707692.html?page=3 further note: Epistemology – Why Should The Human Mind Even Be Able To Comprehend Reality? – Stephen Meyer - video – (Notes in description) http://vimeo.com/32145998bornagain77_{July 18, 2013
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Hmmm competing studies?? America's Blessings: How Religion Benefits Everyone, Including Atheists - Rodney Stark - book Excerpt: Stark devotes whole chapters to unpacking the latest research on how religion affects different facets of modern American life, including crime, family life, sexuality, mental and physical health, sophistication, charity, and overall prosperity. The cumulative effect is that when translated into comparisons with western European nations, the United States comes out on top again and again. Thanks in no small part to America’s rich religious culture, the nation has far lower crime rates, much higher levels of charitable giving, better health, stronger marriages, and less suicide, to note only a few of the benefits. http://www.amazon.com/Americas-Blessings-Religion-Benefits-Including/dp/1599474123 Christians Are Hate-Filled Hypocrites ... and Other Lies You've Been Told - book excerpt: The conclusions drawn here--no surprise--are that the most committed Christians practice what they preach, performing better than the rest of the population on a host of social measures including divorce, domestic violence, sexual misconduct, crime, substance abuse, and everyday honesty. http://www.amazon.com/Christians-Hate-Filled-Hypocrites-Other-Youve/dp/0764207466 Atheism and health A meta-analysis of all studies, both published and unpublished, relating to religious involvement and longevity was carried out in 2000. Forty-two studies were included, involving some 126,000 subjects. Active religious involvement increased the chance of living longer by some 29%, and participation in public religious practices, such as church attendance, increased the chance of living longer by 43%.[4][5] http://www.conservapedia.com/Atheism_and_health Gallup Poll of 676,000 shows the most religious Americans have highest well-being - February 2012 https://uncommondescent.com/religion/gallup-poll-of-676000-shows-the-most-religious-americans-have-highest-well-being/ Look Who's Irrational Now - 2008 Excerpt: "What Americans Really Believe," a comprehensive new study released by Baylor University yesterday, shows that traditional Christian religion greatly decreases belief in everything from the efficacy of palm readers to the usefulness of astrology. It also shows that the irreligious and the members of more liberal Protestant denominations, far from being resistant to superstition, tend to be much more likely to believe in the paranormal and in pseudoscience than evangelical Christians. http://online.wsj.com/article/SB122178219865054585.html There are actually studies that show that people who do not believe in a soul are a little bit more anti-social (psychopathic) than the majority of people who do believe in a soul: Anthony Jack, Why Don’t Psychopaths Believe in Dualism? – video http://www.youtube.com/watch?list=UUmmObUi8Fq9g1Zcuzqbt0_g&feature=player_detailpage&v=XRGWe-61zOk#t=862s Hmm who to believe?? Well seeing that internet atheist have lied to me more times than I can count, I think I'll stick with my studies: As to those elite professors who have more hostility towards their Christian students than other students, even their Muslim students, it might be well for them to remember: The History of Christian Education in America Excerpt: The first colleges in America were founded by Christians and approximately 106 out of the first 108 colleges were Christian colleges. In fact, Harvard University, which is considered today as one of the leading universities in America and the world was founded by Christians. One of the original precepts of the then Harvard College stated that students should be instructed in knowing God and that Christ is the only foundation of all "sound knowledge and learning." http://www.ehow.com/about_6544422_history-christian-education-america.htmlbornagain77_{July 18, 2013
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bornagain @ 12
Thus just for the sake that I love my country and want the people and children of America to be blessed, I support a more Christian America than the hostile one we are faced with today...
I am not American so I have no dog in this fight. However, recent, thorough, published sociological research has compared more-religious to more-secular nations, and more-Christian to less-Christian states within the USA, with the following results: - Secularism is correlated with higher levels of education - Secular nations donate more to poor nations on a per capita basis - In the USA the states with the highest murder rates tend to be highly religious (Louisiana, Alabama), and those with the lowest murder rates tend to be the least religious (Vermont, Oregon) - Rates of all violent crime are higher in religious states in the USA - Murder rates are lower in more secular nations and higher in more religious nations - Nearly all of the top 50 safest cities in the world are in relatively non-religious countries - Atheists are under-represented in the USA prison population (approx 0.2%) - In America agnostics and atheists have lower divorce rates than the religious - Conservative Christian women in Canada suffer higher rates of domestic violence - In the USA teens who undertake religion-inspired virginity pledges are actually more likely to have premarital sex and unprotected sex - The more secular a nation is the higher its reported level of happiness - Religious people are more likely to support the use of torture by governments - Two Holocaust studies found that the more secular people were, the more likely they were to rescue and help persecuted Jews. I don't personally believe secularists are more moral etc. than religious people. However this research does show that pointing the finger at secularism as the cause of social ills is probably not justified.CLAVDIVS_{July 17, 2013
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corrected link: Alison Krauss – Down in the River to Pray http://www.youtube.com/watch?v=vK5okMlZoXQbornagain77_{July 17, 2013
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Thus just for the sake that I love my country and want the people and children of America to be blessed, I support a more Christian America than the hostile one we are faced with today, especially in the education system but also with society at large. Does this mean I favor 'doctoring' the founding fathers beliefs to make them appear as more Christian than they were? No of course not, but it does mean that I severely oppose the secularists attempt to whitewash the Christianity of our founding fathers, especially in regards to the false doctrine of separation of church and state:
The Fallacy Of The Doctrine Of Separation of Church and State - Prager - video http://www.prageruniversity.com/History/The-Separation-of-Church-and-State.html
Of related note, the following video is very interesting as to revealing materialism inability to explain 'knowledge acquisition':
Kurt Godel - Incompleteness Theorem and Human Intuition - video (notes in description of video) http://www.metacafe.com/watch/8516356/
Verse and Music:
Proverbs 9:10 The fear of the LORD is the beginning of wisdom, and knowledge of the Holy One is understanding. Alison Krauss - Down in the River to Pray http://www.youtube.com/watch?v=cvYadad-x5Y
bornagain77_{July 17, 2013
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bb, though you took a swipe at Barton, I want to show you one very important and sobering place where his scholarship has held up: The following video shows that the SAT (Scholastic Aptitude Test) scores for public school students showed a steady decline, for seventeen years from near the top spot in the world, after the removal of prayer from the public classroom by the Supreme Court, not by public decree, in 1963. Whereas the SAT scores for private Christian schools have consistently remained near the top spot in the world:
The Real Reason American Education Has Slipped – David Barton – video http://www.metacafe.com/watch/4318930
You can see the dramatic difference, of the SAT scores for private Christian schools where they have remained high compared to public schools, at this following site;
Aliso Viejo Christian School – SAT 10 Comparison Report http://www.alisoviejochristianschool.org/sat_10.html
Atheists have fought me on this saying that private Christian schools have the advantage of affluence, which is I hold to be a bogus claim, but instead of boring you with financial comparisons, where this SAT statistic gains traction is in looking at the correlating crime trends in America from 1960 onward:
United States Crime Rates 1960 - 2010 (Please note the skyrocketing crime rate from 1963, the year prayer was removed from school, thru 1980, the year the steep climb in crime rate finally leveled off.) of note: The slight decline in crime rate from the mid 90s until now is attributed in large part to tougher enforcement on minor crimes. (a nip it in the bud policy) http://www.disastercenter.com/crime/uscrime.htm AMERICA: To Pray Or Not To Pray - David Barton - crime statistic graphs corrected for population growth http://www.whatyouknowmightnotbeso.com/graphs.html
Perhaps most telling and sad, in the following podcast William Lane Craig, unaware of the strong correlation of the removal prayer from school with other negative statistics, expresses shock at studies which have found the altruism of young people to have declined steadily since the early 1960's
What Lies Behind Growing Secularism by William Lane Craig - May 2012 - podcast (steep decline in altruism of young people since early 1960's) http://www.reasonablefaith.org/what-lies-behind-growing-secularism
Here is another piece evidence,,
Bruce Charlton's Miscellany - October 2011 Excerpt: I had discovered that over the same period of the twentieth century that the US had risen to scientific eminence it had undergone a significant Christian revival. ,,,The point I put to (Richard) Dawkins was that the USA was simultaneously by-far the most dominant scientific nation in the world (I knew this from various scientometic studies I was doing at the time) and by-far the most religious (Christian) nation in the world. How, I asked, could this be - if Christianity was culturally inimical to science? http://charltonteaching.blogspot.com/2011/10/meeting-richard-dawkins-and-his-wife.html
As well, as if that was not sobering enough, I remind you that Christian cultures uniquely provided the conditions necessary for the rise of modern science:
Christianity Gave Birth To Modern Science - Dr. Henry Fritz Schaefer - video http://vimeo.com/16523153
and even though Christianity has this incredible track record of being very conducive for scientific progress, and also being very helpful to the education of our children in America, Christianity is, in spite of this unmatched track record in education and scientific progress, treated with severe prejudice and hostility in higher education.
Majority of American University Professors have Negative View of Evangelical Christians – 2007 Excerpt: According to a two-year study released today by the Institute for Jewish & Community Research (IJCR), 53% of non-Evangelical university faculty say they hold cool or unfavorable views of Evangelical Christians – the only major religious denomination to be viewed negatively by a majority of faculty. Only 30% of faculty hold positive views of Evangelicals, 56% of faculty in social sciences and humanities departments hold unfavorable views. Results were based on a nationally representative online survey of 1,269 faculty members at over 700 four-year colleges and universities. Margin of error is +/- 3%. ,,, Only 20% of those faculty who say religion is very important to them and only 16% of Republicans have unfavorable views of Evangelicals; the percentages rise considerably for faculty who say religion is not important to them (75%) and among Democrats (65%).,,, “This survey shows a disturbing level of prejudice or intolerance among U.S. faculty towards tens of millions of Evangelical Christians,,, One-third of all faculty also hold unfavorable views of Mormons, and among social sciences and humanities faculty, the figure went up to 38%. Faculty views towards other religious groups are more positive: Only 3% of faculty hold cool/unfavorable feelings towards Jews and only 4% towards Buddhists. Only 13% hold cool/unfavorable views of Catholics and only 9% towards non-Evangelical Christians. Only 18% hold cool/unfavorable views towards atheists. A significant majority – 71% of all faculty – agreed with the statement: “This country would be better off if Christian fundamentalists kept their religious beliefs out of politics.” By comparison, only 38% of faculty disagreed that the country would be better off if Muslims became more politically organized. http://www.lifesitenews.com/news/archive//ldn/2007/may/07050808
bornagain77_{July 17, 2013
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Myself, I’m convinced that the founding fathers are far more Christian than the secular revisionists are comfortable with, yet not as fundamental as the extreme right wing would be comfortable with. I envision a ‘common sense’ Christianity of many farmers in America as the overall spirit,, Perhaps if grace allows us, we will be able to talk to a few of the founders when and if we get to heaven to find out the nuts and bolts of the situation.
I agree and I believe Frazer does too. That is what he indicated. Like I said already, according to Frazer, they held Christian morality in high regard and endeavored to live it out. But he didn't find where they recognized Christ for who he was, didn't put faith in his sacrifice and God's grace for salvation, at least in their writing. Who knows what happened on their death beds. I hope it isn't as it appears.bb_{July 17, 2013
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bornagain77,
One thing I am certain of though, and I would think Frazer would agree, is that the secular revisionists who are trying to portray the founders as secularists are also operating from a severe bias of their own.
Gregg did say that. His point was the 8 founders covered in his book, while not Christian, were not secularists either. Like I might describe a Mormon or Unitarian. He also disagreed with the Deist label with a demonstration that each expressed a belief that God acted in the affairs of men where a Deist would say that God created the universe then went on vacation or retired, never to intercede. He said Paine, though not covered in his book, was the only one that matched the definition of Deist. Gregg's presentation was one of two. He has one for Christian groups and one for leftist/liberal groups; each to discourage the group from trying to force "the founders" into their manufactured/preconceived mold. He gave us the Christian version. Gregg seemed to have some problems with David Barton and demonstrated a few instances where Barton force-fit some quotes, with some selective editing, to fit his claim that a founder, that wasn't Christian, was one indeed. The end result in those instances was he made some founders say things they didn't say. Does Barton do this routinely? I don't know.bb_{July 17, 2013
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OT: Matzke's hatchet job on 'Darwin's Doubt' gets regurgitated in New Yorker: How "Sudden" Was the Cambrian Explosion? Nick Matzke Misreads Stephen Meyer and the Paleontological Literature; New Yorker Recycles Misrepresentation - Casey Luskin July 16, 2013 http://www.evolutionnews.org/2013/07/how_sudden_was_074511.htmlbornagain77_{July 16, 2013
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bb, though you are a personal friend of Frazer, and have brought doubt on Fortenberry's scholarship, I'm certainly am not persuaded that Frazer is operating without bias of his own. One thing I am certain of though, and I would think Frazer would agree, is that the secular revisionists who are trying to portray the founders as secularists are also operating from a severe bias of their own.,, Myself, I'm convinced that the founding fathers are far more Christian than the secular revisionists are comfortable with, yet not as fundamental as the extreme right wing would be comfortable with. I envision a 'common sense' Christianity of many farmers in America as the overall spirit,, Perhaps if grace allows us, we will be able to talk to a few of the founders when and if we get to heaven to find out the nuts and bolts of the situation.bornagain77_{July 16, 2013
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bornagain77, OT: I read the review by Bill Fortenberry you referred me to re: Greg Frazer, and I read Fortenberry's booklet, "The Founders and the Myth of Theistic Rationalism". After listening to Frazer's presentation on Sunday, I find that Frazer has much more credibility. To be clear, Greg is an old friend of mine and I know where he stands as a Christian and his motivation. Greg encouraged those there to be careful of anyone that would say "the founders believed..." because they were a diverse group of individuals that had personal views on any number of things. His book is a study on 8 of the founders. He spent the first hour sharing quotes from Adams, Franklin and Jefferson (he didn't have time to cover everyone), regarding key points of Christianity (trinity, deity of Christ, virgin birth, resurrection, salvation by grace). The quotes from the founders mentioned painted the picture of individuals that were not Christian but that respected Christian morality; that saw it necessary for freedom, but not necessarily true in all its claims. And not the only way to God. Fortenberry's booklet is poorly argued. He repeatedly takes a snippet of what Frazer wrote, tells the reader what Frazer meant then takes the reader down a rabbit trail to knock down the straw man constructed. Unrelated to his argument against Frazier, in looking at Fortenberry's website, IncreasingLearning.com, I found a few articles where he describes modern Christian music as using a "voodoo" beat. He concludes that this music can't possibly glorify God because the beat is "Satanic" in origin. Does this mean he can't truthfully argue? No. But it does paint a picture of one whose "research" is undermined by confirmation bias.bb_{July 16, 2013
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So, how many protein-protein binding sites are conservatively found in life? Dr. Behe, on the important Table 7.1 on page 143 of his book 'Edge Of Evolution', finds that a typical cell might have some 10,000 protein-binding sites. Whereas a conservative estimate for protein-protein binding sites in a multicellular creature is,,,
Largest-Ever Map of Plant Protein Interactions - July 2011 Excerpt: The new map of 6,205 protein partnerings represents only about two percent of the full protein- protein "interactome" for Arabidopsis, since the screening test covered only a third of all Arabidopsis proteins, and wasn't sensitive enough to detect many weaker protein interactions. "There will be larger maps after this one," says Ecker. http://www.sciencedaily.com/releases/2011/07/110728144936.htm
So taking into account that they only covered 2%, of the full protein-protein "interactome", then that gives us a number, for different protein-protein interactions, of 310,000. Thus, from my very rough 'back of the envelope' calculations, we find that this is at least 30 times higher than Dr. Behe's estimate of 10,000 different protein-protein binding sites for a typical single cell (Page 143; Edge of Evolution; Behe). Therefore, at least at first glance from my rough calculations, it certainly seems to be a gargantuan step that evolution must somehow make, by purely unguided processes, to go from a single cell to a multi-cellular creature. Moreover as if all that was not bad enough for Darwinists, there is, 'surprisingly', found to be 'rather low' conservation of Domain-Domain Interactions occurring in Protein-Protein interactions:
A Top-Down Approach to Infer and Compare Domain-Domain Interactions across Eight Model Organisms Excerpt: Knowledge of specific domain-domain interactions (DDIs) is essential to understand the functional significance of protein interaction networks. Despite the availability of an enormous amount of data on protein-protein interactions (PPIs), very little is known about specific DDIs occurring in them.,,, Our results show that only 23% of these DDIs are conserved in at least two species and only 3.8% in at least 4 species, indicating a rather low conservation across species.,,, http://www.plosone.org/article/info:doi/10.1371/journal.pone.0005096 What Evidence Is There for the Homology of Protein-Protein Interactions? - 2012 Excerpt: Protein-protein interactions appear to be very rarely conserved unless very high sequence similarity is observed. Consequently, inferred interactions should be used with care… Conclusion excerpt: Using this framework, we are able to estimate interactome sizes with a method that is different from others in the literature. Our estimates for the fraction of conserved interactions are very low for definitions of homology that are often associated with the transfer of functional annotations across species. We emphasise that our results will be overestimates due to the preferential investigation of homologous proteins in multiple species.,,, We urge extreme caution in interpreting interactions transferred across species unless the definition of homology employed is a strict one, and we believe that interactome incompleteness is not solely responsible for the lack of observed conservation of interactions. http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002645
Thus, despite whatever Darwinists may condescendingly say to the contrary, I can find no basis for such false bravado in the power of Darwinian processes in the empirical evidence itself.bornagain77_{July 16, 2013
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Here is a small glimpse of the staggering complexity inherent within the cell that they are trying to explain by a 'it just happened', oops I mean by a 'exaptation', story:
ExPASy - Biochemical Pathways - interactive schematic http://web.expasy.org/cgi-bin/pathways/show_thumbnails.pl
The first problem for Darwinism in explaining such staggering complexity is that Darwinists cannot even explain how a single 'simple' novel protein arises,,
Now Evolution Must Have Evolved Different Functions Simultaneously in the Same Protein - Cornelius Hunter - Dec. 1, 2012 Excerpt: In one study evolutionists estimated the number of attempts that evolution could possibly have to construct a new protein. Their upper limit was 10^43. The lower limit was 10^21. These estimates are optimistic for several reasons, but in any case they fall short of the various estimates of how many attempts would be required to find a small protein. One study concluded that 10^63 attempts would be required for a relatively short protein. And a similar result (10^65 attempts required) was obtained by comparing protein sequences. Another study found that 10^64 to 10^77 attempts are required. And another study concluded that 10^70 attempts would be required. In that case the protein was only a part of a larger protein which otherwise was intact, thus making the search easier. These estimates are roughly in the same ballpark, and compared to the first study giving the number of attempts possible, you have a deficit ranging from 20 to 56 orders of magnitude. Of course it gets much worse for longer proteins. http://darwins-god.blogspot.com/2012/12/now-evolution-must-have-evolved.html?showComment=1354423575480#c6691708341503051454
As if, the probability of finding a novel protein by neo-Darwinian processes were not already overwhelmingly difficult, it is now found that amino acid positions in a protein are interdependent to other amino acid positions in a protein (context dependency), thus exponentially exasperating the 'rarity' problem for neo-Darwinists:
(A Reply To PZ Myers) Estimating the Probability of Functional Biological Proteins? Kirk Durston , Ph.D. Biophysics - 2012 Excerpt (Page 4): The Probabilities Get Worse This measure of functional information (for the RecA protein) is good as a first pass estimate, but the situation is actually far worse for an evolutionary search. In the method described above and as noted in our paper, each site in an amino acid protein sequence is assumed to be independent of all other sites in the sequence. In reality, we know that this is not the case. There are numerous sites in the sequence that are mutually interdependent with other sites somewhere else in the sequence. A more recent paper shows how these interdependencies can be located within multiple sequence alignments.[6] These interdependencies greatly reduce the number of possible functional protein sequences by many orders of magnitude which, in turn, reduce the probabilities by many orders of magnitude as well. In other words, the numbers we obtained for RecA above are exceedingly generous; the actual situation is far worse for an evolutionary search. http://powertochange.com/wp-content/uploads/2012/11/Devious-Distortions-Durston-or-Myers_.pdf
Moreover many times different protein domains must be combined in order to even get a fully functional protein in the first place. What is the ease with which different protein domains are randomly recombined?
Exon Shuffling: Evaluating the Evidence - Jonathan M. - July 2013 The Problems with Domain Shuffling as an Explanation for Protein Folds Excerpt: The domain shuffling hypothesis in many cases requires the formation of new binding interfaces. Since amino acids that comprise polypeptide chains are distinguished from one another by the specificity of their side-chains, however, the binding interfaces that allow units of secondary structure (i.e. ?-helices and ?-strands) to come together to form elements of tertiary structure is dependent upon the specific sequence of amino acids. That is to say, it is non-generic in the sense that it is strictly dependent upon the particulars of the components. Domains that must bind and interact with one another can't simply be pieced together like LEGO bricks. In his 2010 paper in the journal BIO-Complexity Douglas Axe reports on an experiment conducted using ?-lactamase enzymes which illustrates this difficulty (Axe, 2010). http://www.evolutionnews.org/2013/07/an_evaluation_o074441.html Design by Any Other Name - April 9, 2013 Excerpt: One reason for Endy's team's success is the way that they have approached biological systems. Rather than in terms of modular pieces, they took a more integrated approach.,,, Darwinism assumes that organisms are built from the bottom-up, where complexity comes from the incorporation of additional components via chance and selection pressure. An engineering perspective assumes that biological systems are built from the top-down. In other words, the end function is already in mind when the biological system is constructed. Because of this, the system functions as a cohesive whole, rather than as modular components. Furthermore, and as (the success of) Endy's group in particular points out, the parts of the biological systems are not interchangeable like Lego blocks. They have specific functions. Evolutionary theory says that trial and error lead to the biological structures that we see today. But this same trial-and-error method does not work in the laboratory setting, so why should we assume that it worked in nature? http://www.evolutionnews.org/2013/04/design_by_any_o070891.html
What does the hard evidence say about novel protein-protein binding site generation?
"The likelihood of developing two binding sites in a protein complex would be the square of the probability of developing one: a double CCC (chloroquine complexity cluster), 10^20 times 10^20, which is 10^40. There have likely been fewer than 10^40 cells in the entire world in the past 4 billion years, so the odds are against a single event of this variety (just 2 binding sites being generated by accident) in the history of life. It is biologically unreasonable." Michael J. Behe PhD. (from page 146 of his book "Edge of Evolution")
Dr. Behe's empirical research agrees with what is found if researchers try to purposely design a protein-protein binding site:
Viral-Binding Protein Design Makes the Case for Intelligent Design Sick! (as in cool) - Fazale Rana - June 2011 Excerpt: When considering this study, it is remarkable to note how much effort it took to design a protein that binds to a specific location on the hemagglutinin molecule. As biochemists Bryan Der and Brian Kuhlman point out while commenting on this work, the design of these proteins required: "...cutting-edge software developed by ~20 groups worldwide and 100,000 hours of highly parallel computing time. It also involved using a technique known as yeast display to screen candidate proteins and select those with high binding affinities, as well as x-ray crystallography to validate designs.2" If it takes this much work and intellectual input to create a single protein from scratch, is it really reasonable to think that undirected evolutionary processes could accomplish this task routinely? In other words, the researchers from the University of Washington and The Scripps Institute have unwittingly provided empirical evidence that the high-precision interactions required for PPIs requires intelligent agency to arise. Sick! http://www.reasons.org/viral-binding-protein-design-makes-case-intelligent-design-sick-cool Computer-designed proteins programmed to disarm variety of flu viruses - June 1, 2012 Excerpt: The research efforts, akin to docking a space station but on a molecular level, are made possible by computers that can describe the landscapes of forces involved on the submicroscopic scale.,, These maps were used to reprogram the design to achieve a more precise interaction between the inhibitor protein and the virus molecule. It also enabled the scientists, they said, "to leapfrog over bottlenecks" to improve the activity of the binder. http://phys.org/news/2012-06-computer-designed-proteins-variety-flu-viruses.html Protein-Protein Interactions (PPI) Fine-Tune the Case for Intelligent Design - Article with video - April 2011 Excerpt: The most recent work by the Harvard scientists indicates that the concentration of PPI-participating proteins in the cell is also carefully designed. http://www.reasons.org/protein-protein-interactions-fine-tune-case-intelligent-design
bornagain77_{July 16, 2013
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As has become a symbol of many IDist proponents, here C. Hunter first sells the farm, then decides he should try to persuade folks why it should have been sold in the first place. 1) The term 'innovation' has been hijacked by biological scientists. Are we agreed? Etymologically it involves choice, vision, invention, etc. - i.e. human beings innovation. Yet the very same willful hijacking is committed by Dembski himself in his open acceptance of 'technological evolution' (cf. TRIZ). Would Hunter reproach Dembski for his acceptance of 'technological evolutionism' just as he does Wagner here for his views of 'innovation'? To Dembski, 'technology evolves.' What about for Hunter? Hunter has a choice: a) reject the term 'innovation' in biology as an inappropriate naturalistic concept-transfer, or b) accept the language of 'innovation' in biology and then sell IDT as an improperly packaged attempt to speak about agency, purpose and teleology, which are already long discussed and ripe in non-natural sciences. 2) Hunter has chosen to part with the farm, freely giving 'innovation' to biological science, then faults his target of choice 'evolution' as the guilty objective (impersonal) 'theory.' It is a similar move to how many IDists reify the concept-duo 'I+D' conveniently forgetting that it is a 'theory' (IDT) only. Yet since he is stuck on the 'fact/theory' notion of American PoS wrt creationism and evolutionism, for Hunter there seems to be no possibility of moving forward. Just dig in one's feet and pull backpeddling against ideology. Nevertheless, I'm glad Hunter speaks of 'tension.' Indeed, it is like a relatively young flock of IDists (i.e. IDM) willfully tugs on their (culture warring) cord of IDT against 'Darwinism'. A simple finger pull against them (by a non-Darwinist) would topple the lot and, more importantly, release the tension.Gregory_{July 16, 2013
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Classic example of "Intelligent Evolution". Just replace the designer with evolution, and tell a credible story to the world.
The origin of feathers, which help with stabilization during flight. But they probably originated for completely different reasons such as thermal insulation or waterproofing. There are also these fascinating proteins in our eye lens called crystallins, which originated from metabolic enzymes. At high concentrations they retain transparency, allowing nature to build lenses with high refractive indices, which are well suited to focus light.
Cristian Pascu_{July 16, 2013
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It seems they studied the metabolism of e-coli. Here are few related notes on metabolism that don't sit well with Darwinian just so stories: Optimal Design of Metabolism - Dr. Fazale Rana - July 2012 Excerpt: A new study further highlights the optimality of the cell’s metabolic systems. Using the multi-dimension optimization theory, researchers evaluated the performance of the metabolic systems of several different bacteria. The data generated by monitoring the flux (movement) of compounds through metabolic pathways (like the movement of cars along the roadways) allowed researchers to assess the behavior of cellular metabolism. They determined that metabolism functions optimally for a system that seeks to accomplish multiple objectives. It looks as if the cell’s metabolism is optimized to operate under a single set of conditions. At the same time, it can perform optimally with relatively small adjustments to the metabolic operations when the cell experiences a change in condition. http://www.reasons.org/articles/the-optimal-design-of-metabolism Life Leads the Way to Invention - Feb. 2010 Excerpt: a cell is 10,000 times more energy-efficient than a transistor. “In one second, a cell performs about 10 million energy-consuming chemical reactions, which altogether require about one picowatt (one millionth millionth of a watt) of power.” This and other amazing facts lead to an obvious conclusion: inventors ought to look to life for ideas.,,, Essentially, cells may be viewed as circuits that use molecules, ions, proteins and DNA instead of electrons and transistors. That analogy suggests that it should be possible to build electronic chips – what Sarpeshkar calls “cellular chemical computers” – that mimic chemical reactions very efficiently and on a very fast timescale. http://creationsafaris.com/crev201002.htm#20100226a This stunning energy efficiency of a cell is found to be optimal across all life domains, thus strongly suggesting that all life on earth was Intelligently Designed for maximal efficiency in mind instead of reflecting a pattern of somewhat random distribution that would be expected if evolution occurred: Mean mass-specific metabolic rates are strikingly similar across life's major domains: Evidence for life's metabolic optimum Excerpt: Here, using the largest database to date, for 3,006 species that includes most of the range of biological diversity on the planet—from bacteria to elephants, and algae to sapling trees—we show that metabolism displays a striking degree of homeostasis across all of life. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2572558/ Also of interest is that the integrated coding between the DNA, RNA and Proteins of the cell apparently seems to be ingeniously programmed along the very stringent guidelines laid out by Landauer’s principle, by Charles Bennett from IBM of Quantum Teleportation fame, for ‘reversible computation’ in order to help achieve such amazing energy efficiency. Notes on Landauer’s principle, reversible computation, and Maxwell’s Demon - Charles H. Bennett Excerpt: Of course, in practice, almost all data processing is done on macroscopic apparatus, dissipating macroscopic amounts of energy far in excess of what would be required by Landauer’s principle. Nevertheless, some stages of biomolecular information processing, such as transcription of DNA to RNA, appear to be accomplished by chemical reactions that are reversible not only in principle but in practice.,,,, http://www.hep.princeton.edu/~mcdonald/examples/QM/bennett_shpmp_34_501_03.pdf The amazing energy efficiency possible with ‘reversible computation’ has been known about since Charles Bennett laid out the principles for such reversible programming in 1973, but as far as I know, due to the extreme level of complexity involved in achieving such ingenious ‘reversible computation’, has yet to be accomplished in any meaningful way for our computer programs even to this day:bornagain77_{July 16, 2013
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