@pauluc: You wrote: Nowhere however do you answer the real question

Comment on LSU memorandum confirms Educate Truth’s allegations by Sean Pitman.

You wrote:

Nowhere however do you answer the real question that was posed to David Read. You are implying that the creationist argument is correct simply because the alternative is deficient. I know this is the SOP but I had hoped that you would be proactive in telling me whey this data is best interpreted from a creationist perspective which was David Reads contention.

Nested Hierarchical Patterns (NHPs) can be explained by both common descent with mindless modification over time and by deliberate design. Many human designed systems, like object oriented computer programming for example, show NHPs.

So, how does one tell if a given NHP is the result of mindless mechanisms or the result of deliberate design? Well, one must actually investigate various features of the pattern itself to see if all of the features associated with the pattern can be adequately explained by any known non-deliberate mechanism. If some aspect of the pattern cannot be explained by a known non-deliberate mechanism, but is still within the realm of deliberate design, the ID-only hypothesis can rationally be invoked at that point. Once it is known that deliberate design was most likely involved with the production of at least some aspect of the NHP in question, it is also reasonable, at that point, to suggest that the overall NHP itself may have been deliberately designed as well.

In the case of living things, they are indeed generally arranged in a NHP – a “Tree of Life” (ToL) so to speak. Again, the NHP itself can be produced by mindless mechanisms or by deliberate design. So, what aspect of the ToL would be beyond the realm of any known mindless mechanism? – given that the NHP itself can be produced by mindless mechanisms?

As noted previously, the functional differences between living things and even subsystems within living things, beyond very low levels of functional complexity, can only be explained, at the current time, by intelligent design. There is no currently known mindless mechanism that can produce qualitatively novel functional information beyond very low levels of functional complexity.

Since every living thing demonstrates very high levels of functional complexity, the ID-only hypothesis can rationally be invoked to explain the origin of life. And, since many different types of living things have qualitative functional differences as well, these high level qualitative differences can also be most rationally explained by the ID-only hypothesis.

Once one demonstrates that intelligence was most certainly in play in the origin of numerous aspects of the ToL, one can also rationally propose that the overall NHP was also the likely result of deliberate design.

How can the apparently unplanned but cobbled together and functional mess that is the genome be best explained in a creationist framework? It cries out chance and contingency which is precisely what evolution would predict and why it is increasingly seen as the most compelling by most genome scientists. As you know you will not replace this dominant model by carping about minor or major deficiencies because in science you know a model is not replaced because it is deficient but because there is a better model.

Real science demands that models be at least theoretically falsifiable. That means that a particular model can be shown to be false even if there is no other model with which to replace the current model. A false model is a false model. It’s as simple as that.

Beyond this, your notion that the genome is a hodge-podge poorly planned jumbled mess is a view that is at odds with the currently emerging view of the genome – a fractal view if you like where the more closely it is investigated, the more and more intricate and complex it appears. What might initially appear to be a “mess” of circuits, wires, and microchips might later turn out to be a cutting edge supercomputer designed by the most advanced minds in computer science. The only reason why someone might initially interpret their work as a “mess” is because of the initial ignorance of the observer.

In other words, the concept of a “mess” is subjective – it is in the eye of the beholder. This “messy” notion of yours certainly isn’t objective science. Just because you wouldn’t do it that way doesn’t mean it wasn’t intelligently designed. And, if you can’t do as good yourself, you probably aren’t qualified to describe something as “a mess” or “poorly designed” to begin with. Richard Dawkins got into this embarrassing situation when he described the inverted human retina as an obvious example of poor design… later shown to be an ingenious design (to include the fairly recently discovered fiber-optic Mueller cells).

In light of your “poor-design” argument, consider the following thoughts of Erika Hayden on the intricacies of the genome and how clueless modern scientists have been in their understanding of it:

“We fooled ourselves into thinking the genome was going to be a transparent blueprint, but it’s not,” says Mel Greaves, a cell biologist at the Institute of Cancer Research in Sutton, UK. Instead, as sequencing and other new technologies spew forth data, the complexity of biology has seemed to grow by orders of magnitude. Delving into it has been like zooming into a Mandelbrot set — a space that is determined by a simple equation, but that reveals ever more intricate patterns as one peers closer at its boundary….

“It seems like we’re climbing a mountain that keeps getting higher and higher,” says Jennifer Doudna, a biochemist at the University of California, Berkeley. “The more we know, the more we realize there is to know.”…

Researchers from an international collaborative project called the Encyclopedia of DNA Elements (ENCODE) showed that in a selected portion of the genome containing just a few per cent of protein-coding sequence, between 74% and 93% of DNA was transcribed into RNA. Much non-coding DNA has a regulatory role; small RNAs of different varieties seem to control gene expression at the level of both DNA and RNA transcripts in ways that are still only beginning to become clear. “Just the sheer existence of these exotic regulators suggests that our understanding about the most basic things — such as how a cell turns on and off — is incredibly naive,” says Joshua Plotkin, a mathematical biologist at the University of Pennsylvania in Philadelphia.

Erika Check Hayden, Human genome at ten: Life is complicated, Nature 464, 664-667, Published online 31 March 2010

Sean Pitman Also Commented

LSU memorandum confirms Educate Truth’s allegations
@pauluc:

perhaps you could give us your analysis of this paper and how the data supports your creatonist perspective?

1. Liu GE, Alkan C, Jiang L, Zhao S, Eichler EE. Comparative analysis of Alu repeats in primate genomes. Genome Res 2009 May;19(5):876-885.

What are the “actual facts” here?
What is the guesswork and what is the unproven axiom.
What is the creationist interpretation of this?

The facts:

SINEs, to include Alu repeats, are indeed short interspersed sequence elements of ∼300 nt in length, propagating within a genome through retrotransposition and account for ∼10% of the human genome sequence. They also have an impact on phenotypic change via alternative splicing, genomic rearrangements, segmental duplication, and expression regulation causing disorders like Hunter syndrome, hemophilia A, and Sly syndrome.

The guesswork:

The proposed evolutionary relationships over deep time based on nested hierarchical patterns is just-so story telling without scientific value. Such stories have no useful predictive value nor are they effectively falsifiable.

Part of the problem here is that the paper you reference treats SINE insertions as “homoplasy-free character states in cladistic analyses of primates.” The assumption isn’t true. According to Cantrell, et at., SINE insertions are simply not homoplasy-free phylogenetic markers since they are subject to hot-spot insertions independent of phylogenetic relationships.

Cantrell, Michael A. and others. 2001. An Ancient Retrovirus-like Element Contains Hot Spots for SINE Insertion. Genetics 158:769-777.

In any case, there really are no “foolproof” genetic markers of common decent. All of the ones proposed so far to be foolproof have been shown to have significant flaws. The prediction that pseudogenes, transposons (SINEs and LINEs) and other shared mutational mistakes are conclusive evidence for common descent has not held up. For example, consider the following excerpt from David Hillis’ paper entitled, “SINEs of the perfect character.” published in the Proceedings of the National Academy of Sciences, 1999:

What of the claim that the SINE/LINE insertion events are perfect markers of evolution (i.e., they exhibit no homoplasy)? Similar claims have been made for other kinds of data in the past, and in every case examples have been found to refute the claim. For instance, DNA-DNA hybridization data were once purported to be immune from convergence, but many sources of convergence have been discovered for this technique. Structural rearrangements of genomes were thought to be such complex events that convergence was highly unlikely, but now several examples of convergence in genome rearrangements have been discovered. Even simple insertions and deletions within coding regions have been considered to be unlikely to be homoplastic, but numerous examples of convergence and parallelism of these events are now known. Although individual nucleotides and amino acids are widely acknowledged to exhibit homoplasy, some authors have suggested that widespread simultaneous convergence in many nucleotides is virtually impossible. Nonetheless, examples of such convergence have been demonstrated in experimental evolution studies.

Beyond this, the assumption that SINEs and other such sequences could not have originally served any beneficial purpose (i.e., that no reasonable designer would have deliberately included them within the primate genome) has also been shown to be false.

In a Science article by Wojciech Makalowski, the following comments are made that seem to echo what design theorists have been saying for a very long time:

Although catchy, the term “junk DNA” for many years repelled mainstream researchers from studying noncoding DNA. Who, except a small number of genomic clochards, would like to dig through genomic garbage? However, in science as in normal life, there are some clochards who, at the risk of being ridiculed, explore unpopular territories. Because of them, the view of junk DNA, especially repetitive elements, began to change in the early 1990s. Now, more and more biologists regard repetitive elements as genomic treasure.”

Makalowski, Wojciech. 2003. Not Junk After All, Science 300:1246-1247

As it turns out, a lot of beneficial and even critical functionality has been identified for SINEs, LINEs, pseudogenes, and other various kinds of genetic sequences that were once thought to be “Junk DNA”; remnants of mistakes of a long evolutionary history of trial and error. There are also sequences which don’t seem to have any function, yet remain identical between very different species.

For example, in May of 2004 Haussler and Bejerano used computers to compare the human genome with the mouse and the rat genomes. They were surprised to find long stretches of shared non-coding “junk” DNA that were exactly the same in humans and rodents.

“There were about five hundred stretches of DNA in the human genome that hadn’t changed at all in the millions and millions of years that separated the human from the mouse and the rat,” says Haussler. “I about fell off my chair. It’s very unusual to have such an amount of conservation continually over such a long stretch of DNA.”

Many of these stretches of DNA, called “ultraconserved” regions, don’t appear to code for protein, so they might have been dismissed as junk if they hadn’t shown up in so many different species. Haussler “confirmed that negative selection is three times stronger in these regions than it is for nonsynonymous changes in coding regions.” As far as Haussler is concerned, “It is a mystery what molecular mechanisms would place virtually every base in a segment of size up to 1 kilobase [i.e., 1000 bp] under this level of negative selection”. That’s 500 regions of DNA up to 1000 bp that are identical between rats and humans – up to 500,000 identical genetic sites in DNA?! What is also surprising is that these same regions largely matched up with chicken, dog and fish sequences as well; but are absent from sea squirt and fruit flies. Note that the last supposed common ancestor for all of these creatures was thought to live some 400 million years ago.

“From what we know about the rate at which DNA changes from generation to generation, the chance of finding even one stretch of DNA in the human genome that is unchanged between humans and mice and rats over these hundred million years is less than one divided by ten followed by 22 zeros. It’s a tiny, tiny fraction. It’s virtually impossible that this would happen by chance.”

Of course, this is in light of an interesting experiment described by Nóbrega et. al. in a 2004 issue of the journal Nature where the authors demonstrated that large-scale deletions (two large non-coding intervals: 1,511 kilobases and 845 kilobases in length for a total of 1,243,000 bp) of non-coding DNA could be tolerated by mice without any detectible functional effect. “Viable mice homozygous for the deletions were generated and were indistinguishable from wild-type littermates with regard to morphology, reproductive fitness, growth, longevity and a variety of parameters assaying general homeostasis.” What is especially interesting here is that these particular non-coding sequences are conserved between humans and rodents. The authors argue that, “Some of the deleted sequences might encode for functions unidentified in our screen; nonetheless, these studies further support the existence of potentially ‘disposable DNA’ in the genomes of mammals.”

The problem here is the question of why such “disposable DNA” would be so conserved over many tens of millions of years? Functional or non-functional, it still poses a problem for standard evolutionary theory. If functional, it isn’t non-functional remnants of evolutionary trial and error history and fits well within design theory. If non-functional its high degree of conservation doesn’t seem to fit with the idea that many tens of millions of years have actually passed since the ancestral origin of either humans or rodents (or chickens, dogs, and fish).

Even so, those like Haussler and Nóbrega still believe very strongly that humans and rats do in fact share a common ancestor that lived a hundred million years ago or so. The idea that perhaps humans and rats might have actually been individually created, deliberately, does not even cross their minds.

In short, such patterns do not falsify the ID-only hypothesis since they do not even address the origin of high levels of functional information within the genomes of living things. Also, the age of various genomes is often calculated based on mutation rates that are actually calculated based on prior evolutionary assumptions. Real time studies of mutation rates have shown that these assumptions are off by as much as 20 or even 100 fold.

http://www.detectingdesign.com/dnamutationrates.html

Then, there is also the problem of the rapid degeneration of the functional elements in the genomes of slowly reproducing species – humans, other primates, and all other mammals for that matter. All such gene pools are devolving, not evolving. They are declining in quality – i.e., they are headed for extinction at a fairly rapid rate.

http://www.detectingdesign.com/dnamutationrates.html#Detrimental

Such evidence calls into serious question the validity of these just-so stories of mainstream scientists when it comes to their explanation of the nested hierarchical patterns that they find in various genomes.

For more information on this topic see:

http://www.detectingdesign.com/pseudogenes.html

http://www.uncommondescent.com/intelligent-design/daniel-fairbanks-cherry-picks-data-on-pseudogenes-to-prop-up-common-descent/

Sean Pitman
www.DetectingDesign.com

Recent Comments by Sean Pitman

Science and Methodological Naturalism
Very interesting passage. After all, if scientists are honest with themselves, scientific methodologies are well-able to detect the existence of intelligent design behind various artifacts found in nature. It’s just the personal philosophy of scientists that makes them put living things and the origin of the fine-tuned universe “out of bounds” when it comes to the detection of intelligent design. This conclusion simply isn’t dictated by science itself, but by a philosophical position, a type of religion actually, that strives to block the Divine Foot from getting into the door…

Revisiting God, Sky & Land by Fritz Guy and Brian Bull
@Ron:

Why is it that creationists are afraid to acknowledge the validity of Darwinism in these settings? I don’t see that these threaten a belief in God in any way whatsoever.

The threat is when you see no limitations to natural mindless mechanisms – where you attribute everything to the creative power of nature instead of to the God of nature.

God has created natural laws that can do some pretty amazing things. However, these natural laws are not infinite in creative potential. Their abilities are finite while only God is truly infinite.

The detection of these limitations allows us to recognize the need for the input of higher-level intelligence and creative power that goes well beyond what nature alone can achieve. It is here that the Signature of God is detectable.

For those who only hold a naturalistic view of the universe, everything is attributed to the mindless laws of nature… so that the Signature of God is obscured. Nothing is left that tells them, “Only God or some God-like intelligent mind could have done this.”

That’s the problem when you do not recognize any specific limitations to the tools that God has created – when you do not recognize the limits of nature and what natural laws can achieve all by themselves.

Sean Pitman
www.DetectingDesign.com

Revisiting God, Sky & Land by Fritz Guy and Brian Bull
@Bill Sorensen:

Since the fall of Adam, Sean, all babies are born in sin and they are sinners. God created them. Even if it was by way of cooperation of natural law as human beings also participated in the creation process.

God did not create the broken condition of any human baby – neither the physical or moral brokenness of any human being. God is responsible for every good thing, to include the spark or breath of life within each one of us. However, He did not and does not create those things within us that are broken or bad.

“The owner’s servants came to him and said, ‘Sir, didn’t you sow good seed in your field? Where then did the weeds come from?’ ‘An enemy did this,’ he replied. “The servants asked him, ‘Do you want us to go and pull them up?'” Matthew 13:27-28

Of course, all humans are indeed born broken and are in a natural state of rebellion against God. However, God is not the one who created this condition nor is God responsible for any baby being born with any kind of defect in character, personality, moral tendency, or physical or genetic abnormality. God did not create anyone with such brokenness. Such were the natural result of rebellion against God and heading the temptations of the “enemy”… the natural result of a separation from God with the inevitable decay in physical, mental, and moral strength.

Of course, the ones who are born broken are not responsible for their broken condition either. However, all of us are morally responsible for choosing to reject the gift of Divine Grace once it is appreciated… and for choosing to go against what we all have been given to know, internally, of moral truth. In other words, we are responsible for rebelling against the Royal Law written on the hearts of all mankind.

This is because God has maintained in us the power to be truly free moral agents in that we maintain the Power to choose, as a gift of God (Genesis 3:15). We can choose to accept or reject the call of the Royal Law, as the Holy Spirit speaks to all of our hearts…

Remember the statement by Mrs. White that God is in no wise responsible for sin in anyone at any time. God is working to fix our broken condition. He did not and does not create our broken condition. Just as He does not cause Babies to be born with painful and lethal genetic defects, such as those that result in childhood leukemia, He does not cause Babies to be born with defects of moral character either. God is only directly responsible for the good, never the evil, of this life.

Sean Pitman
www.DetectingDesign.com

Revisiting God, Sky & Land by Fritz Guy and Brian Bull
@Ron:

Again, your all-or-nothing approach to the claims of scientists isn’t very scientific. Even the best and most famous of scientists has had numerous hair-brained ideas that were completely off base. This fact does not undermine the good discoveries and inventions that were produced.

Scientific credibility isn’t based on the person making the argument, but upon the merits of the argument itself – the ability of the hypothesis to gain predictive value when tested. That’s it.

Sean Pitman
www.DetectingDesign.com

Gary Gilbert, Spectrum, and Pseudogenes
Don’t be so obtuse here. We’re not talking about publishing just anything in mainstream journals. I’ve published several articles myself. We’re talking about publishing the conclusion that intelligent design was clearly involved with the origin of various artifactual features of living things on this planet. Try getting a paper that mentions such a conclusion published…

Sean Pitman
www.DetectingDesign.com