On saving it for marriage II:Non-theist edition

7 Reasons Why Atheists Wait Until Marriage

August 14th, 2011 by Leo
Why on earth would an atheist ever choose to wait until they were married to engage in the wonderfully pleasurable world of sex!? Well I happen to be an atheist and I happen to have decided to wait until I’m married. Does this make me crazy? Maybe. But here’s a list of 7 very sane, very logical reasons that suggest otherwise.

1. Logic

Logic might seem like a strange reason for a person to wait until they’re married but when we examine the statistics it makes much more sense. Couples that do wait have only a fraction of the divorce rate that others do. I personally think divorce would be a miserably unpleasant thing to experience and would like to increase my chances of a successful union wherever I can. Couples who wait also enjoy better communication, rank their relationships as more fulfilling, and even claim to enjoy BETTER SEX. If I’m being perfectly honest, anything that even slightly promises better sex in a lifelong partner seems worth pursuing. So looking at things objectively it does make sense to wait.

2. Setting an Example

Although sex is a private thing, your decision to wait doesn’t have to be. In fact you can use your decision to influence others you care about. According to the statistics mentioned above anyone who waits has a better chance at a successful marriage. I personally want my own children and even my siblings and friends to have the best shot at a happy marriage possible. I have a little sister and I don’t want her to grow up seeing her brothers sleep their way through the local population. Others that are inspired by you will hopefully go on to inspire their own children and friends. It feels good to set such a positive example!

3. Healthy Self Image

Does sex make you feel better about yourself? I have no idea. What I do know is that many people do look for sex for the self-esteem boost it can provide. Knowing what you want in life (such as a strong relationship) leads to higher self-awareness and in turn a higher self-esteem. If you know yourself then it’s highly unlikely that you’ll feel the need to seek out sexual relationships for a pick me up. Having control over your image is a powerful thing indeed. It gives you the razor sharp focus you need to pursue other goals like education, a career, and meaningful relationships.

4. Rebellion!

I personally love this reason. In a culture that is steeped in cheap sleazy dime-a-dozen sex I like to be the one that smirks at everyone else. I go to the same bars and clubs as everyone else does but when I see them all grinding like rabbits in heat I can take pride in the fact that I am not one of them. Nonreligious individuals are already rebelling against something so it’s only natural that they would withdraw even further from the majority.

(Or as a modern philosopher put it "it's hip to be square.")

5. Respect

Respect goes two ways. The first is the idea that I respect my future wife (even though we’ve probably never met) enough that I want her to take solace in the knowledge that I am all hers. I think most girls would agree that a guy who has waited for them is pretty cool. That goes both ways. Guys will think it’s pretty awesome too! The second reason I abstain out of respect is because most girls are going to be someone’s future wife! I respect those will-be unions enough to not interfere. Plus I don’t want guys pushing themselves on my wife to be!

6. Idealism

One definition of idealism states, “conforming to an ultimate standard of perfection of excellence; the idea of something that is perfect; something that one hopes to attain.” While idealism is a highly romantic notion, it is universally shared by people that are waiting, religious or otherwise. We all are seeking that perfect union, that ultimate standard of perfection. The idea of ‘the one,’ a single person that will compliment you better than anyone else is highly idealistic. While a person may experience love in many relationships throughout their lives reserving physical intimacy for only one of those loves places it above the rest.

Dedicating one’s life to an ideal — especially one that aims to make another person feel so special — is a very unique and selfless choice. It will make whoever chooses to follow this path feel like they are on a quest. While it will not be easy eventually the person they wind up with will love them all the more for it.

7. Poetry

While this may seem very similar to idealism it is really the essence of the ideal mind. Poetry is the heart and soul of waiting. It is the romance, the true love, the life partner; these things all sing poetry. Living a poetic life is to live for beauty itself. When we see elderly couples holding hands we can’t help but sigh. It is comforting to see two people, so in love, after so much time. Beauty is inspirational and for this reason more than any others on this list is why someone who is nonreligious might choose to wait. Without the ideal of heaven, and the everlasting love of an eternal father there isn’t a whole lot of beauty left in the world. Except for one thing. Love.

On saving it for Marriage III:The gold standard

Benefits in Delaying Sex Until Marriage
Happier Marriages, More Satisfying Sex Among the Perks, Study Finds
By Bill Hendrick
WebMD Health News Reviewed by Louise Chang, MD
WebMD News Archive

What’s more, couples who delay sex until their wedding night have more stable and happier marriages than couples who have premarital sex, according to the study, which appears in the Journal of Family Psychology.

The study involved 2,035 married participants in an online assessment of marriage called “RELATE.” According to the study, people who waited until marriage:

rated sexual quality 15% higher than people who had premarital sex
rated relationship stability as 22% higher
rated satisfaction with their relationships 20% higher

The benefits were about half as strong for couples who became sexually active later in their relationships but before marriage.

Developing Relationship Skills

“Most research on the topic is focused on individuals’ experiences and not the timing within a relationship,” study author Dean Busby, PhD, a professor in Brigham Young University’s School of Family Life, says in a news release. “There’s more to a relationship than sex, but we did find that those who waited longer were happier with the sexual aspects of their relationship.”

It may be that couples report greater satisfaction and sexual quality if they’ve waited because the extra time gives them longer to learn about each other and develop the skills necessary for good relationships, Busby says.

About 92% of the respondents had attended college, 32% completed some college, 24% obtained a bachelor’s degree, and the average age was 36. The majority of the couples had sex within two months of starting to date, while 16% delayed intercourse until marriage.

Prioritizing Sex at Start of Relationship May Not Be Optimal

Mark Regnerus, PhD, of the University of Texas, who wasn’t involved with the study, says it suggests to him that couples who “prioritize sex promptly at the outset of a relationship often find their relationships underdeveloped when it comes to the qualities that make relationships stable and spouses reliable and trustworthy.”He is the author of a forthcoming book titled “Premarital Sex in America,” being published by Oxford University Press.

Busby and colleagues controlled for the influence of religious involvement in their analysis because it often plays a role on when couples choose to initiate sex. “Regardless of religiosity, waiting helps the relationship form better communication processes, and these help improve long-term stability and relationship satisfaction,” Busby says.

The study says 21% of respondents were Catholic, 39% Protestant, 6% Latter-Day Saints (Mormon), 17% members of “another religion,” and 17% who indicated no religious affiliation. The authors write that sexual intimacy in the early stages of dating is sometimes viewed as an important part of testing compatibility, and determining whether a relationship would work later on.

But the researchers say their findings are clear, that “the longer a couple waited to become sexually involved, the better that sexual quality, relationship communication, relationship satisfaction and perceived relationship stability was in marriage ...”

Higher Ed demystified?

Toward a theory of devolution II

Devolution: Getting Back to the Simple Life
Denyse O'Leary

As we have seen already in this series, evolution can occur via horizontal gene transfer and epigenetics, both of which add information to a life form by non-Darwinian means -- that is, not by natural selection acting on random mutation of the genome.The information added by epigenesis and horizontal gene transfer is not random. For example, assume that male parents' alcoholism is consistently associated with disrupted patterns in children's genes. The effects of excess alcohol, far from being random, are a predictable, law-like chain of chemical cause and effect. Similarly, bacteria don't randomly share antibiotic resistance via horizontal gene transfer. Rapid development of resistance among whole colonies is a longstanding, law-like pattern that maintains a colony's ecology, a pattern recently traced back to millennia before humans began to develop antibiotics.

Today, we often hear that these non-random mechanisms of evolution are consistent with Darwinian evolution (the Modern Synthesis). So, nothing has really changed after all!

Not so fast. Darwinian evolution (Darwinism) had better be consistent with all demonstrated mechanisms of change. Unlike horizontal gene transfer, it has proven difficult to witness, and proponents have relied largely on the assumption that it is "the only known theory that is in principle capable of explaining certain aspects of life." What's changed is that it can no longer be considered equivalent to "evolution." It must compete with other known mechanisms.

Most of the time, when we think of evolution, we mean mechanisms for the growth of complex new information. After all, entropy (the tendency for disorder to increase over time) can satisfactorily explain loss of information. Yet, in the history of life, some forms survive while -- or even by -- losing information (devolution). Their history may tell us something useful too.

We all know devolution when we see it -- a jar of pennies becomes a doorstop, a computer becomes a boat anchor, the XYZ volume of the Encyclopedia props up a too-short table leg.

But interest in devolution of life forms spiked with the recent discovery of giant viruses, which a 2014 editorial at The Scientist considered a possible fourth domain of life.

The giant mimivirus for example, unlike conventional viruses, "carries many genes thought to be unique to cellular life, suggesting that it evolved from a cell."
If so, strictly speaking, it "devolved" from a cell. Information was lost, not gained. Perhaps the unicellular life form was unable to survive intact, but some remnant survives as a virus.

New Scientist announced in 2011 that, "World's largest virus proves giants came from cells." The idea is a reasonable one, though some, including National Geographic, now think that giant viruses preceded cells instead. We don't really know as yet.

The viruses have, however, infected researchers with incorrect thoughts. A discoverer of a giant virus encased in ice for 30,000 years observed (2014):

"We thought it was a property of viruses that they pack DNA extremely tightly into the smallest particle possible, but this guy is 150 times less compacted than any bacteriophage [viruses that infect bacteria]. We don't understand anything anymore!"
Didier Raoult, the discoverer of giant Marseillevirus said, provocatively, in 2009, "The idea of a common ancestor makes no sense in the light of viruses. That was Darwin's idea, but he was clearly wrong." Raoult, also the discoverer of the mimivirus (2003), considered "the most productive and influential microbiologist in France" according to Science, published a pop science book in 2011 that "flat-out declares that Darwin's theory of evolution is wrong."

Well, here are some things we can be reasonably sure of:

-- Sometimes, devolution offers an apparent advantage. Many plankton microbes eliminated the genes for producing key vitamins, and now outsource the function. One account suggests, "... most of the time, the fitness advantages of smaller genomes and lower cell replicating costs offset the potential fitness gains that would come from vitamin manufacture when the required nutrients are in short supply." Similarly, while functioning cell walls are thought to be critical to life forms, we are told that many bacteria can switch to a cell wall-deficient "L-form" state, "completely resistant to many antibiotics," and possibly ignored by our immune systems.

-- Similarly, some researchers believe that the Amanita mushroom group has devolved to a successful parasite on trees by losing the genes associated with breaking down cellulose. It's possible that the Amanitas were crowded by ground-level competitors and devolution enabled them to exploit a new niche.

-- Sometimes, however, the advantage is not clear. A brain part, the anterior sclerite, present in arthropods of 500 million years ago, is no longer extant. It is thought to be linked with bulbous eyes, but without further information, it's impossible to say why it is apparently no longer required.

-- Similarly, the Cambrian shrimp's heart (520 mya) was more complex than the modern one: "The level of complexity of the Fuxianhuia was extremely high, considering that we are studying some of the oldest animals on Earth." A 305-million-year-old harvestman (spiderlike arachnid) fossil has two sets of eyes (pictured above), but current descendants have one functional pair and one vestigial pair, apparently without suffering any adverse effect. But we would need to know much more than we do about the history of life to know why decreasing complexity was neutral or advantageous in each case.

-- One devolved amphibian is visually almost indistinguishable from an earthworm. Similarly, a newly discovered blind, legless lizard is described as having "evolved to live underground," though again, that should really be devolved.

-- Sometimes a pattern emerges. A study that investigated evolution in nematode worms, including the strain that survived the 2003 Columbia space shuttle crash, shows that under artificially stressed lab conditions, the worms all lost the same gene.

In some cases, particular aspects of Darwinian evolution have proved false by discoveries of devolution. One Darwinian doctrine, called Dollo's Law, formulated about 1890 by Belgian paleontologist Louis Dollo, states that a trait once lost cannot be regained.

No one seems to have told the life forms about it. For example, researchers were surprised to find one creature:

... in the aquifers beneath the Western Australian desert, which challenges the traditional Darwinian view of evolution. They have discovered that a species of blind predatory water beetles -- living underground for millions of years -- express vision genes (opsin) which are usually only found in species with eyes.
Losses can be reversed. Blind Mexican cavefish are considered an excellent model for studying evolution, with revealing results. In the lab, researchers have mated blind cave fish from separate and distant underwater caves and produced sighted offspring. Apparently, separate mutations had produced the blindness, and some hybrid offspring inherited a mix that includes enough genes for functioning sight. So no irrevocable devolution had taken place after all.

We are told that, with "dwindling evidence for the law-like nature of Dollo's Law" opinions are reversing because "large genomics databases and evo-devo studies are showing how the underlying developmental pathways and genetic architecture can be retained after the loss of a character."

Evolutionary biologists still have an odd relationship with devolution, to judge from items in Scientific American over the last two decades. First, we encounter obfuscation:

From a biological perspective, there is no such thing as devolution. All changes in the gene frequencies of populations -- and quite often in the traits those genes influence -- are by definition evolutionary changes.
...

Another misconception is that increasing complexity is the necessary outcome of evolution. In fact, decreasing complexity is common in the record of evolution. For example, the lower jaw in vertebrates shows decreasing complexity, as measured by the numbers of bones, from fish to reptiles to mammals. (Evolution adapted the extra jaw bones into ear bones.) Likewise, ancestral horses had several toes on each foot; modern horses have a single toe with a hoof.

This approach doesn't quite make sense. It fudges the fact that loss and gain of information are not the same thing. Loss needs no explanation other than entropy; gain requires new sources of complex, specified information.

Even writers in the same publication seem to contradict themselves about the existence of devolution. In 2012, a Scientific American blog reported on a new study that argued humans are devolving so as to be dumber: "Homo (Sans) Sapiens: Is Dumb and Dumber Our Evolutionary Destiny?"

Gerald Crabtree, a biologist at Stanford University, has put forward a provocative hypothesis that our cushy modern existence -- absent the ceaseless pressures of natural selection experienced during the Paleolithic -- makes us susceptible to the slow creep of random genetic mutations in the 2,000 to 5,000 genes needed to ensure that our intellectual and emotional makeup remains intact.
Others, we were told, disagree with Crabtree: The social world we live in is complex, so "we haven't in fact lost the selection process that kept the pressure on" to remain intelligent. But if Darwinian natural selection both produces high intelligence, and is needed to sustain it, why did it work only once, for humans? And does anyone really believe that social rejection today is the same as the life-and-death struggles of the Paleolithic?

In 2014, Scientific American, on a more serious note, informed us, with respect to those blind cave fish:

In the classic view of evolution, organisms undergo random genetic mutations, and nature selects for the most beneficial ones. A recent study in Science adds a twist to that theory: variability already present in a population's genome may remain hidden in times of plenty but come unmasked in stressful situations, ready to help with adaptation.
This is, we are told, still "a topic of active research." That is a good approach, better than insisting that traditional Darwinian concepts offer all the insight we need as long as we can cut the subject down to size. Because, one way or another, it's just not Darwin's evolution any more.

A variety of other non-Darwinian mechanisms of evolution may produce some change in some life forms, and we shall shortly give them each their turn in the spotlight.

Toward a theory of devolution. I

Michael Behe’s Darwin Devolves Topples Foundational Claim of Evolutionary Theory

Brian Miller

Editor’s note: Darwin Devolves is currently being sold by preorder. The limited-time offer includes a new 41-part online course with Michael Behe, a bonus chapter, and an exclusive, national conference call. You can and should preorder here right now.

I saw at the website Peaceful Science that biologist Nathan Lents, author of Human Errors: A Panorama of Our Glitches, from Pointless Bones to Broken Genes, says that he has been asked to review Mike Behe’s new book, Darwin Devolves: The New Science About DNA That Challenges Evolution (DD). Professor Lents notes:

I’ve been commissioned to review Behe’s new book, out next year, so I am reading it now. I’m about 70 pages in and so far, all I’ve seen is, “Gee, this stuff is complicated!”

Lents can rest assured: There is far more to the book than that. Behe dismantles the fundamental claim of evolutionary theory that mutations and natural selection naturally drive life toward greater complexity as new information is constantly generated. In stark contrast to this belief, Behe demonstrates the opposite. He summarizes the thesis of his book by stating 

With surpassing irony it turns out that…Darwinian evolution proceeds mainly by damaging or breaking genes, which, counter-intuitively, sometimes helps survival. In other words, the mechanism is powerfully de-volutionary. It promotes the rapid loss of genetic information. Laboratory experiments, field research, and theoretical studies all forcefully indicate that, as a result, random mutation and natural selection make evolution self-limiting. That is, the very same factors that promote diversity at the simplest levels of biology actively prevent it at more complex ones. Darwin’s mechanism works chiefly by squandering genetic information for short-term gain. 

Several Red Flags

Behe begins by describing several red flags that demonstrate how evolutionary claims often represent a pretense of knowledge without real substance. For instance, in statements such as

…every cell has evolved mechanisms that identify and eliminate misfolded and unassembled proteins. 

one could simply remove the word “evolved” and no meaning would be lost. In other words, most evolutionary accounts include no significant details, so they provide no actual knowledge. 

Behe then describes several wonders of nature, such as insects with gears, bacteria that construct internal magnets out of toxic materials, and special cells in eyes that act as fiber optic cables tuned to specific wavelengths of light. I found this section particularly captivating. It also provided a stark contrast between the innovations seen in nature and natural selection’s observed limitations. 

The Core Argument

The following section lays out the core argument of the book which centers on the empirical data gleaned from the most thorough studies of evolution on the molecular level. Such research has only become possible in the last twenty years since new technology has enabled sequencing of DNA on large numbers of organisms. For the first time, evolutionary claims can be properly tested, and Behe presents the most rigorous analysis to date based on hard data. He describes research on numerous organisms including the following iconic examples:

Darwin’s finches: Approximately a dozen species of finches on the Galápagos island descended from a single species over a period of two million years. 

Cichlid fishes: About 500 species of cichlid fishes in Lake Victoria evolved from a single species over a period of 15,000 years. Similar numbers of species evolved from single species in Lake Malawi over a few million years and in Lake Tanganyika over 10 million years. 

E. coli: Approximately 60,000 generations of E. coli were studied by Richard Lenski’s research group. They periodically froze samples, so the changes in DNA could be mapped throughout the populations’ histories.  

All studies demonstrated the same basic results. First, the vast majority of adaptive mutations degrade or outright disable genes. For instance, the gene most strongly associated with the difference in blunt-beak verses pointed-beak finches is called ALX1. The only variation in it throughout all finch species is two mutations that both impair function. Similarly, the E. coli strains that best adapt to strong selective pressures primarily disable genes that are not immediately needed for survival. Behe labels this result the First Rule of Adaptive Evolution:

Break or blunt any gene whose loss would increase the number of offspring. 

First Rule of Adaptive Evolution

This rule is easy to understand. Random mutations can far more easily break a gene than enable some new function, so solutions to challenges that involve breaking a gene will predominate. An analogy Behe uses is a person whose house is filling up with water due to a leaky pipe. The available options are to break a hole in the wall to allow the water to escape or wait for a pump to be delivered that happens to be on a ten-year backorder. The obvious solution would be to break a hole in the wall. 

Second, mutations that modify a function are far fewer and represent trivial changes. For instance, the most widely publicized result from Lenski’s lab was the appearance of strains of E. coli that were able to eat citrate. However, the bacteria already have this ability. It is normally switched off in the presence of oxygen. The fortunate bacteria obtained an alteration that allowed them to access citrate in all conditions. The third observation is that mutations which initiate new functions or modify existing ones still usually lead to the loss of significant quantities of genetic information. In the previous example, the citrate-eating bacteria developed additional mutations which resulted in the loss of function in several other genes. In the end, the strains fine-tuned their metabolism to the new environment, but at the expense of losing the ability to survive in the original one. As another example, the bacteria that caused the Black Death in the 14th century evolved from a free-living benign species that lives in the soil. However, it acquired new genetic information from another bacteria which allowed it to live in a human host. In the new environment it quickly lost numerous genes which confined it to a parasitic lifestyle. 

A relatively small number of beneficial mutations do occur that do not incur negative costs, but they always represent miniscule changes. For instance, certain species of cichlid fish obtained a mutation in a rhodopsin protein which allowed for greater sensitivity to light at greater, versus lesser, water depths. But the new protein only differed from the original by a single amino acid. This single alteration represents the most impressive feat of evolution in one of biologists’ most prized case studies over a period of time comparable to that in which the largest transformations took place in the fossil record. Contrast this change with the hundreds, if not thousands, of coordinated mutations that are required to construct the fiber optic eye cells mentioned above. 

The Big Picture

The big picture conclusions of all studies is that evolutionary processes are only capable of driving changes at the level of species and genera, but not at the level of families or higher. Stated differently, evolution produces a limited number of changes and then no further significant change is possible. For instance, the adaptations seen in the cichlid fish in Lake Victoria over 15,000 years closely match those seen in the cichlid fish in the other lakes after several million years. The same limited number of changes repeated themselves over and over. In addition, all modifications represent minor alterations of the same cichlid body plan. 

The evidence commonly cited to argue for evolution’s ability to drive large-scale transformations is almost always circular. Biologists regularly identify similarities and differences between two groups and then assume those differences are the result of natural selection, mutations, and related processes. However, this conclusion is not based on any actual hard evidence. It is simply assumed. As Behe demonstrates, all empirical data point to the conclusion that evolution is only capable of producing minor alterations of existing designs but nothing truly novel. Evolutionists must now to an even greater extent disconnect their grand narratives from empirical data and confine them to the realm of their unrestrained imaginations. Anyone interested in knowing the truth about the design/evolution debate will find Darwin Devolves a must read. 

Yet More on clarity in the design debate.

In Arguments for Intelligent Design, Definitions and Assumptions Are Important
Ann Gauger

How can random non-coding DNA be, at the same time, both functional (as in the genome) and non-functional (as in extremely unlikely to code for functional proteins)?

   This question was posed recently at Peaceful Science, a discussion site that seeks to promote dialog between atheists, theistic evolutionists, and proponents of intelligent design. (Their success is mixed. ID proponents often feel like Aragorn in the last battle.) It’s a good question. It came out of a conversation about orphan genes, where I was arguing that non-coding DNA was extremely unlikely to give rise to a new coding sequence with any function. Yet ID people claim all the time that the majority of the genome is functional.. How can sequence be both functional and non-functional at the same time? The answer turns on two things. The meaning of “function” and clarity about what’s being tested.

I had been trying to explain Doug Axe’s results to the group of debaters, most of whom did not agree. According to Axe, sequences that can produce a functional protein, namely a protein capable of carrying out an enzymatic reaction, are extremely rare. (They could be rare in number and/or rare in how far apart they are spread in sequence space.) 

Picture a Bank Vault

Think of a situation where you have to crack the code on a bank vault, with many dials in the code, say 150, each specifying 1 out of 10 digits. If there is only one code that will work, the number of possible sequences to try is 10^150, Now say that 100 sequences out of 10^150 would work. That reduces the number you would have to try. It would now be 10^148.

What’s the solution? Well, suppose there was another bank next door, that had a similar code, in fact with 125 of the dials identical! And you happened to know that code. Now the information required is greatly reduced. You have only 10^25 to get. Likely success? And if you are very lucky and know the code nearly completely, all but 3 dials (maybe you know the teller or the person who built the vault), it is definitely easier to break the code. 10^3 =10 x 10 x 10. You have a pretty good chance of success.

The problem is worse for proteins. They have twenty possible amino acids for each position in a protein, so the total possible sequences for a protein 150 amino acids long is 20^150.

To do a random search through that whole space of 20^150 is not possible, just like it would be impossible to search through the 150 dials to find the bank code. But if proteins are not far apart in sequence space, like the bank code where almost all of the code was identical to another bank’s code, then the chances of finding a sequence that will work are greatly improved.

A Crime Spree

Now consider one more thing. Suppose suddenly there were bank robberies everywhere, and it wasn’t by force. The dials had been turned to the correct combinations. What would be your inference? I would say that someone knew the codes.

So unless functional sequences are easy to find (very common), and/or are clustered together (easily reachable from one functional island to another), explaining current protein diversity without design is impossible.

I’ll break that down.

“Unless functional sequences are easy to find (very common), and/or are clustered together (easily reachable from one functional island to another)”: I am laying out the conditions where it might be possible to find function.

“Explaining current protein diversity without design is impossible”: Unless the above conditions are met, namely that functional sequences are easy to find or clustered together, we won’t be able to find functional sequences, unless design has been involved.

Now turn the sentence around.

Explaining current protein diversity without design is impossible, unless functional sequences are easy to find (very common), and/or are clustered together (easily reachable from one functional island to another).

As a consequence, if we find that apparently random non-coding sequences have given rise to new genes and proteins in many genomes, in fact representing 10-30 percent of the genomes analyzed, that result should surprise us, given what I said above. But we need additional evidence still. See below.

Now for the other half of the problem or confusion here. In ENCODE, scientists claimed that the majority of our DNA was functional, meaning it had some sign of biochemical activity. Transcription, methylation, a site for DNA binding, etc., any of these would qualify as functional in some sense. But even ENCODE workers admit they don’t know how much of that “function” will be meaningful.

In the ENCODE sense, most genomic sequence is functional, thus functional sequence is common (20-80 percent was the original range offered). Just remember what function means here — biochemical function, not sequence coding for functional proteins.

So Which Is It? 

If the genome is functional in the sense of ENCODE, that agrees with one part of ID. Some of us argued that the genome would not be junk. We would expect some kind of function for most of it.

But being functional in the biochemical sense (à la ENCODE) does not mean it is easy to give rise to new genes and proteins. When we say functional sequence is rare in sequence space, we mean a different sort of function and sequence than in ENCODE. We mean a sequence that can have the ability to carry out an enzymatic reaction. It is our claim that proteins made from random sequence will rarely if ever have any sort of enzymatic activity. 

That is why experimental tests are to be desired. Can random DNA sequence produce functional proteins with enzymatic activity or not? If experiments say no, that implies something extra is going on, because we do see lots of de novo genes.

However, such experiments may be impossible, because of the inability to test enough sequence to get a handle on a likely small signal. Proving a negative is always difficult. None of the protocols I know can screen enough sequences to test Doug’s hypothesis. 

However, if it is easy to get a functional enzyme from random DNA, if there should be a positive result,  that would definitely argue that de novo genes may be the product of natural processes, and not necessarily design.

As I said earlier, there are labs examining this question of the difficulty of getting enzymatic function from random sequence. I look forward to their results.

There is more that could be said here but I’ll save it for another time.

Reproduction v. Darwin.

Why Evolution and Reproduction Are Unnatural
Granville Sewell

In a recent American Spectator article, “Evolution — More Certain than Gravity?”,Sarah Chaffee and I made the point that to not believe in intelligent design, you have to believe that the four fundamental, unintelligent forces of physics alone (the gravitational, electromagnetic, and strong and weak nuclear forces) could have rearranged the fundamental particles of physics on our once-barren planet into encyclopedias and science texts and computers and airplanes and Apple iPhones.

In a 2017 Physics Essays article, “On ‘Compensating’ Entropy Decreases,” I argued that this spectacular increase in order seems to violate the more general statements of the second law of thermodynamics; at least that you cannot dismiss this claim, as is always done, simply by saying that the Earth is an open system and order can increase in an open system. You have to argue that the increase in order is not really extremely improbable given what has entered our open system from outside.

Darwinists Are Not Impressed

Whether or not you believe that what has happened on Earth violates the second law, I can’t imagine anything in all of science that is more clear and more obvious than that unintelligent forces alone cannot produce such things as Apple iPhones. But Darwinists are not impressed. They believe that natural selection, alone among all natural causes, can create spectacular order out of disorder, and even produce beings that can write science texts and design computers.

That it seems even superficially plausible (until we think about the details) that selection could create such order out of disorder relies completely on the fact that living things are able to reproduce, that they are able to preserve their complex structures and pass them on to their descendants without significant degradation, generation after generation. Without reproduction, there are no variants to select from. Reproduction is the most fundamental characteristic of life. We see it happen everywhere, so we may feel there is nothing “unnatural” about reproduction. 

Imagine Self-Reproducing Cars

But to appreciate how unnatural the astonishing reproductive abilities of living things really are, imagine trying to design cars that are able to give birth to other cars. Although it is far beyond our current technology, imagine that it were possible to construct a fleet of cars that contained completely automated car-building factories inside, with the ability to construct new cars — and not just normal new cars, but new cars containing automated car-building factories inside them. If we left these cars alone and let them reproduce themselves for many generations, is there any chance we would eventually see major advances arise through natural selection of the resulting duplication errors? 

Of course not. Without intelligent humans there to fix the mechanical problems that would inevitably arise, the whole process would grind to a halt after a few generations. We are so accustomed to seeing animals make copies of themselves without significant degradation that we dismiss this as just another “natural” process. But if we actually saw cars with fully automated car factories inside, making new cars with car factories inside them, maybe we would realize what an astonishing process reproduction really is. “How do these instruction sets not make mistakes as they build what is us?” asks mathematician Alexander Tsiaras in the wonderful TED Talk:

How indeed? If you — understandably — cannot accept that something we see happen every day should be called “unnatural,” please watch the video.

The Limits of Natural, Unintelligent Forces

It is not only unnatural that species should evolve from simple to complex, it is unnatural even that they should not degrade over time. Individuals of each species do in fact decay into simpler components, as soon as they die — that is what “natural” looks like. Thus even if the transitions between major groups of animals could be made without encountering irreducible complexity (they certainly cannot), there would still be something very unnatural about evolution, and it still could not be explained without intelligent design. The argument for intelligent design could not be simpler or clearer: natural, unintelligent forces of physics alone cannot rearrange atoms into computers and airplanes and Apple iPhones. Any attempt to explain how they can must run up against reality somewhere, because they obviously can’t.

A Postscript on the Second Law

I hesitate to bring the second law back into this debate because of the controversy it always generates. But people sometimes say that the second law only requires that order should not increase (entropy should not decrease), it does not require that order must actually decrease, so there is nothing unnatural about species simply maintaining their complex structures and passing them on generation after generation without significant degradation. Yet common sense tells us that, when only natural forces are at work, complex things must degrade, and slowly only if everything is almost “frozen in time” (nothing is changing), or else they are already degraded to nearly simplest form. 

Obviously, neither of these conditions holds for the case of animal reproduction. Common sense is actually confirmed by the equations of entropy change when we consider the application of the second law to diffusion of a substance X. Notice that since usually J = -D*gradient(C), equation A7 of my Physics Essays article (equation A4 for the case where X-entropy is just thermal entropy) says that if “X-order” is not imported from outside (the boundary integral term is zero), the only way X-order cannot decrease rapidly is when either things are almost frozen in time (the diffusion coefficient D is small), or the X-order is already close to the minimum possible (gradient(C) is small).

Darwinism:Where success is an orphan?

About Orphan Genes — What’s the Big Problem for Evolution?
Ann Gauger

Orphan genes — genes that are present in only one species, or a group of closely related species — are of particular interest to advocates of intelligent design. The reason for this has to do with the assumptions of evolutionary biology.

The main evolutionary assumption is common descent, that all life is descended from one or a few ancestors. Following from this, and taken as evidence for this, is the assumption that all life shares DNA in common. Prior to the advent of widespread genome sequencing, it was assumed that living things shared genes, that there was a set of shared housekeeping genes, and a set of genes specific to a taxonomic group, though these would be few in number. It was assumed that the vast majority of genes would be found multiple places in the genomes of living things. The reason? It was assumed that getting new genes was hard, and once a workable solution was found it would be preserved in the descendants that followed. The bulk of genes would have been invented early in evolution, and thus would be broadly shared.

When It All Changed

But all that changed when many genomes were sequenced and their transcripts analyzed. Each genome, or each taxonomic group, such as bivalves or insects, was found to contain unique genes, found only in that group or species. This was a surprise. At first it was attributed to incomplete sampling. As more genomes were sequenced, it was thought, the uniqueness would turn out to be illusory. Other organisms would carry those genes. As a related explanation, the sparsity of their distribution might be due to horizontal gene transfer, or to gene loss. The hypothesis was that what appeared to be unique was so because it was the result of some rare transfer between species, and we hadn’t identified the source. Or what once was widespread had been lost over evolutionary time.

These explanations are not proving true. First, the more genomes that are sequenced, the more the proportion of orphans should shrink, as more and more “orphans” should be shown to be present in other genomes. But that has not proven to be the case. The mountain of orphan genes is growing, not shrinking. Similarly, horizontal gene transfer was not born out. The sister genes of orphans should have been found as sample size increased, reducing the proportion of orphan genes. As for gene loss as an explanation, it would have to be too massive to be realistic to account for the patterns seen.

One last possibility. The orphans could be related to other genes, but their sequences could have diverged so much as to be unrecognizable. Only their protein structures might reveal relatedness. This also has not been born out by studies that have determined structures of orphan proteins.

A Sea Change in Evolutionary Thinking

So what’s the solution? If you are an evolutionary biologist, it’s simple. You decide it must be easy to get new genes directly from random (non-coding) DNA, or by frameshift or overlapping genes (which amounts to random sequence). This represents a sea change in evolutionary thinking.

Now hold it. Saying that it’s easy to get new genes from DNA by those methods overturns a major Darwinian expectation. In 1977, in his famous article “Evolution and Tinkering,” which has been cited many thousands of times, the Nobel laureate François Jacob explained the accepted view of how evolution constructed new genes:

…once life had started in the form of some primitive self-reproducing organism, further evolution had to proceed through alterations of already existing compounds. New functions developed as new proteins appeared. But these were merely variations on previous themes. A sequence of a thousand nucleotides codes for a medium-sized protein. The probability that a functional protein would appear de novo by random association of amino acids is practically zero. In organisms as complex and integrated as those that were already living a long time ago, creation of entirely new nucleotide sequences could not be of any importance in the production of new information. 

New genes must arise from pre-existing genes, leaving the signal of ancestry in their closely related (i.e., homologous) sequences, because the probability of the alternative is “practically zero.” That’s why the discovery of orphan genes, which show no homology to other sequences, came as a great surprise.

No Problem, You Say?

“No problem. Isn’t that what science supposed to be about?” said one evolutionist to me. “Adapting your theory to fit the facts?”

Well, theories have to be amenable to falsification too. They can only bend so far.

So how can we tell whether genes are easy to get or hard? By testing these alternatives in the lab.

At present the preferred theory for the birth of new genes is to take a stretch of DNA that is currently not being transcribed into RNA, then let it acquire the signals necessary for transcription, then have that new transcript have a function, either as an RNA or after being translated into protein. 

This is in fact how many orphan genes are found. An RNA transcript is made in one species from a stretch of DNA that in a sister species does not make RNA. Further work then determines if the RNA is translated into protein, and ultimately, if the protein has a function.

But in order for this scenario for orphan gene creation to work, functional protein sequences have to be easy to acquire, within reach of an evolutionary search starting from an existing non-functional stretch of DNA. Evolutionists tend to think that such a thing happens easily. Evolutionary processes can produce a new gene or structure or chemical activity easily. This must be true if evolutionary processes are the explanation for orphan genes.

The Rarity of Functional Protein Folds

In contrast, ID proponents think that it’s very difficult to get function from random sequence. There’s a definite reason for this. Experiments by Dr. Douglas Axe measured the rarity of functional protein folds in sequence space (only 1 in 10^77 proteins form a fold with a target function, a very, very, very small number). If functional proteins are very rare in sequence space, that makes it very difficult to get new genes or structures or chemical activities. Others have found similar answers, when asking for the requirements to produce an enzymatic activity. Others, when asking for simple kinds of activity, like sticking to a column loaded with a substrate like ATP, get numbers that are conceivably within range of evolutionary processes. Just sticking to a column is not nearly as demanding as carrying out an enzymatic reaction. 

There are strong points of view as to the reliability of the various methods. How the various experiments are judged tends to be influenced by one’s particular view on the question of evolution. So the best thing is to do more experiments, which is precisely what the scientific community is doing. 

Work is in progress now in many labs to test the question of how hard it is to get an orphan gene from non-coding sequence. Some are asking how hard it is to get a promoter (necessary to promote active transcription). Some are asking how likely it is for random sequence to have function. The sticking point, literally, seems to be that random sequences don’t fold properly and are insoluble in water. They aggregate. That makes most kinds of function difficult, to say the least. Lastly, how likely is it that the function will actually be helpful? We’ll see.

The answer is not in. If Doug Axe is right (and remember, he is not the only researcher to have found that functional proteins are very rare in sequence space), then getting an orphan gene by an evolutionary process is extremely unlikely. But orphan genes are possible, maybe even to be expected, when a designing intelligence acts.

Someday we'll look back and laugh.

Our Hairlessness: Another Evolutionary Enigma Suggestive of Intelligent Design

David Klinghoffer March 18, 2013 2:53 PM

Nina Jablonski, Penn State anthropologist and author of Skin: A Natural History, gives an interesting interview to CNN on how our presumed pre-human ancestors lost their fur. It's a bit of a puzzle because (per the conventional set of evolutionary assumptions and deductions) our ancestors were furry like chimps, and Jablonski reasons that they lost their fur so as to allow for improved sweating required by the innovation of our becoming excellent long-distance runners.

CNN: When did we first lose our fur and gain this pigmentation?

Jablonski: The human lineage evolved in Africa. If we start at a starting point of 6 to 7 million years ago, when humans first parted ways from the ancestors of chimpanzees, we have a lot of fossils that indicate that humans were walking on two legs, but they were not modern-looking. They were fairly short, and they still had quite ape-like body proportions: fairly long arms, relatively short legs. These were Australopithecus species of various kinds. They were good bipeds, but they were also capable tree-climbers. But when we look at their skeletons in detail, it's pretty clear that they were not active runners. They could walk on two legs but they weren't running or striding purposefully across the savanna most of the time, they were sort of living lives that are much like those of chimpanzees: fairly close to the edge of the forest, sometimes going into trees for protection, and then walking for short distances in the open to forage.

We hypothesize that, at that stage in our lineage's evolution, we still would have had quite a bit of body hair, because the reason we started to lose body hair is related to the need for controlling body heat.

It turns out that primates lose most of their heat through radiation from the surface of the body into the environment, and by evaporation of sweat. The hotter it is outside, the more important sweat becomes, especially if the animal is exercising vigorously and generating a lot of internal body heat. Internal body heat is good to a point, but you have to be able to liberate excess heat, otherwise your brain, organs and muscles get too hot.

Primates as a lineage almost exclusively use sweating for this purpose (versus other mechanisms such as panting). There have been a lot of hypotheses made about why we lost most of our body hair. And I definitely, and many colleagues of mine definitely are of the opinion -- based on the environmental, anatomical and genetic evidence at hand -- that we lost most of our body hair because of the needs of heat regulation.

But as Jablonski also points out, chimps beneath their fur have light-colored skin. Take away the fur and you've a light-colored animal that, in the hot African sun, would be extremely vulnerable to the damaging rays of the sun. So you need dark skin. But what would the evolutionary advantage of that be before the transition to going furless? None that's apparent. So which came first?

The running? But that requires the furless feature (not to mention a massive investment in tightly coordinated anatomical reengineering under the skin, as Ann Gauger discusses in Science and Human Origins). The furless feature then? But that requires the dark skin. OK so the dark skin came first? But that seems to somehow look forward to future usefulness before any evolutionary advantage comes into play, which in turn sounds dangerously teleological.

Darwinian evolution can't just put things like that in the bank, with a view toward their being helpful in some future stage of the evolving lineage. Such anticipation, on the other hand, is a hallmark of intelligent design as we're all familiar with it from daily life. Otherwise, blind Darwinian churning seems to have got very lucky in pulling off these three simultaneous innovations just at the right time, together. That sounds more like an illustration of design innovation, doesn't it?