Eviscerating an Anti-ID Argument

A member of Telic Thoughts named Mark Frank commented about detecting design in this thread. Frank also mentioned having authored an article at the Talk Reason website. An article by Frank entitled, An account of how we detect design, is the focus of this blog entry.

A remark referencing the World Trade Center Twin Towers is quoted from the article.

"Suppose the twin towers had been hit not by planes but by two meteors, large enough to seriously damage the towers, and for the purposes of this fantasy suppose the meteors had no physical connection that we could discern -- they were from different sources and were following unrelated trajectories. Such meteor strikes are less frequent than commercial airplanes flying into buildings -- remember Schipol. So the probability of two such meteors striking the same location in the same day is even smaller than two planes striking the same location. Yet we would hesitate to ascribe the two meteors to design."

This is reasonable. Read the intervening part up to this remark which follows:

"In the second case of the meteors we are much less inclined to accept the design explanation -- even though the likelihood of it being accidental are even smaller -- because the idea of a designer who can control meteor strikes is so wildly implausible. We cannot conceive how they could do it."

First, control of a meteor is not as implausible as Frank would have you believe. It should be a possibility for a species like our own with access to a future technology. But what Frank has presented is a classic argument from personal incredulity. He cannot conceive of a designer having such a capacity and is eager to dismiss a design option based on that. Suppose instead of two meteors it had been four or eight. At what point does personal incredulity give way to empirical observations? There was a time in history when the idea that rocks fell out of the sky was ridiculed. It seemed so counter intuitive. Quantum physics, predictions of relativity and multiple universes seem counter intuitive to many as well. Let's look at this next quote:

"ID concentrates on just one thing: the improbability of the outcome given that the cause is chance." It does not address the likelihood of the rival causes existing (chance or design)."

This is clearly erroneous. As evidenced by ideas promoted at Telic Thoughts and elsewhere, it is our knowledge of the nature of existing systems that leads us to impute design. The above also would lead one to believe that Darwinian theories can be assessed based on selected chance events or deterministic causal factors. While an evolutionary process would allow an assessment based on this, an abiogenesis scenario would not. Darwinists simply do not have a theory of origins characterized by causal specificity. Unlike an evolutionary scenario, containing fully functional organisms and a natural selection paradigm as a key theoretical component, the origin of life has no natural mechanism known to generate cells. This is a critical point for, unlike the Twin Towers example, we have no identifiable cause empirically demonstrating an option that could be labeled counter design.

In addition we do have an identifiable property of cells that quacks like a designed duck- the symbolic encoding sequences of nucleotides found in DNA. Codons represent amino acids as well as the command sequences (initiate transcription, stop etc.) as a consequence of a genetic code that allows assigment of symbolism. The coding system parallels symbolic encoding systems known to be intelligently generated. The next comment merits a response as well.

"It goes even further than that. It explicitly forbids any exploration of design as a cause because it refuses to be drawn into who or what the designer is or how they implement their design."

Also untrue. IDists will go as far as evidence suggests to identify a designer. You simply do not need an exact identity to infer a designed event. What is inferred in the case of DNA is an intelligent cause because that is consistent with the nature of the information storage nucleic acid.

There is one more point needing mention. Anti-IDists have gone to considerable efforts to impose legal consequences for designer IDing that infers a deity. In the United States the separation clause is the weapon of choice. However, while on the one hand critics seek government enforcement of a no God option, with the other they call attention to an alleged reluctance to identify a deity. It's a good strategy if you can get away with it.

How Unique is Earth?

28 New Exoplanets Discovered tells us about the continual addition of new planets to an ever growing list of extra-solar planets. We know enough already to appreciate the uniqueness of earth in our universe. It is difficult even to locate planets with conditions that would allow for life. Yet it is planets which could be hospitable to life that are the most intriguing. If life arose on earth, why would it not do the same everywhere in the universe where conditions reasonably approximate those on prebiotic earth?

A designer centered cosmological outlook could explain earth's unique status and make predictions as to the likehood of finding life elsewhere in the universe. A non-designer outlook is pegged to environmental factors. Here is the opening paragraph at the linked website:

"Astronomers have discovered 28 new planets outside of our solar system, increasing to 236 the number of known exoplanets, revealing that planets can exist around a broad spectrum of stellar types-from tiny, dim stars to giants."

Swimming Dinosaurs

A news release of The Geological Society of America entitled, Definitive Evidence Found of a Swimming Dinosaur, refers to evidence that dinosaurs could swim. From the news item:

"According to co-author Loic Costeur, Laboratoire de Planétologie et Géodynamique de Nantes, Université de Nantes, France, the S-shaped prints paint a picture of a large floating animal clawing the sediment as it swam in approximately 3.2 meters of water. Ripple marks on the surface of the site indicate the dinosaur was swimming against a current, struggling to maintain a straight path.

"The dinosaur swam with alternating movements of the two hind limbs, a pelvic paddle swimming motion," said Costeur. "It is a swimming style of amplified walking with movements similar to those used by modern bipeds, including aquatic birds."

The question of whether dinosaurs could swim has been researched for years. Until now, however, very little hard evidence existed documenting the behavior. Several earlier discoveries were later found to have been produced on dry ground or categorized as ghost traces, possible undertracks preserved in lower layers of sediment."

Righting Wrong Conceptions About ID

Top Misconceptions about Intelligent Design is a short article that refutes some common misconceptions about intelligent design. Don't expect the errors to disappear though for those that propagate them have a vested interest in continuing the propaganda.

Addressed are the phoney standbys such as ID being creation in sheep's clothing or, as others would put it, a Trojan Horse. Another is the drummed up expectation of optimal or perfect design. Then there is the God of the Gaps cliche which opponents of ID are to utter from time to time like an initiation slogan. Finally, there is the allegation that ID and evolution are, of necessity, warring concepts. Critics mean philosophical materialism but that's another post. The article is available at the link.

Emotional Animals

An article from NewScientist entitled Do animals have emotions? has some good anecdotes for those of us who love animals. Animals do experience emotions as those of us who have pets would know. But wild anumals experience a gamut of emotions as well. Romping playfully through fields, preening each other and caring for disabled members of a herd characterize observed animal behavoir.

I've gotten to know some pets well during my life and have come to value their individuality as well as the sometimes interesting interrelationships they form. Some are more aggressive than others and some more affectionate. There appears to be clear differences in intelligence among pets of the same species too.

Evolutionary explanations for altruism and other forms of behavoir are all too often of an ad hoc nature. Predictions based on them are also difficult to pin down. On the other hand viewing animals from a telic perspective is both more satisfying and more productive in my view.

An Important New Study Impacting Our Understanding of DNA Repair

Analysis Reveals Extent of DNA Repair Army is an article of the Howard Hughes Medical Institute which highlights the importance of genomic repair mechanisms; an important theme of this blog. The article, which notes a new study and its related publication in the journal Science, reveals some surprising findings noted by the study's senior author Stephen J. Elledge of Harvard. Quotes from the article in green:

"But precisely how cells monitor the integrity of their genomes, identify problems, and intervene to repair broken or miscoded DNA has been one of nature's closely held secrets. Now, however, a report in the journal Science describes a new database developed by a team of researchers from the Howard Hughes Medical Institute at Harvard Medical School that is providing the first detailed portrait of the army of more than 700 proteins that helps maintain DNA's integrity."

700 proteins involved in maintaining genomic integrity! The essential nature of the function is underlined by the sheer number of proteins involved. More from the article:

"The DNA damage response is a routine event in the life of any cell. Stress caused by environmental factors such as exposure to ultraviolet light, ionizing radiation or other environmental phenomena can cause DNA to break apart or rearrange its nucleotide base pairs in unhealthy ways. If such mutations are left unchecked, they can accumulate over time and lead, ultimately, to cancer or diabetes."

Note the consequences of unrepaired damage to DNA. It is actually more severe than indicated here. Damaged genomes produce defective proteins and impaired regulatory functions.

"Elledge explained that two critical enzymes, known in scientific shorthand as ATM and ATR, act like sensors to detect trouble and initiate the DNA damage response by engaging the cell's molecular repair apparatus."

Before an effective response to a problem can be mounted there must be a recognition that the problem exists. The essential nature of individual proteins is indicated by their functions.

"The results of this study illustrate the extraordinarily broad landscape of the DNA damage response, which extends far beyond what was anticipated from previous studies," he said."

Another indication of the importance of DNA repair. It clearly impacts medicine and should do the same with respect to theories about the origin and diversification of life.

"The proteins, known as Abraxas and RAP80, bind to the BRCA1 protein and form a complex that governs three essential modes of DNA damage control: damage resistance, genetic checkpoints that constrain cell proliferation, and DNA repair. There are three variants of this BRCA1 complex and one is mediated by Abraxas and RAP80, providing potentially different windows into the protective nature of the gene.

“We have to stop thinking about BRCA1 as a single entity. There are three complexes and which complex is doing what? That's what needs to get figured out,” Elledge said.

He noted that simply knowing that BRCA1 comes in three distinct flavors gives researchers the chance to sort out the role of each in the DNA damage response and the onset of tumors."

A pattern that is well entrenched in the history of research. Increasing knowledge is associated with the discovery of ever increasing biological complexity. Three varieties of BRCA1 correspond to three types of damage control: damage resistance, constraining cell proliferation by means of genetic checkpoints and DNA repair. This appears to be a sub-system in which all parts are needed to maintain effective genomic repair.

These are exciting research findings which alter our conception of just how vast and intricate is the network of proteins involved in containing DNA damage, as Elledge so aptly pointed out.

Overlapping Protein Coding Regions

A research article entitled A First Look at ARFome: Dual-Coding Genes in Mammalian Genomes authored by Wen-Yu Chung1, Samir Wadhawan1, Radek Szklarczyk2, Sergei Kosakovsky Pond3, and Anton Nekrutenko1 contained this interesting opening paragraph:

Coding of multiple proteins by overlapping reading frames is not a feature one would associate with eukaryotic genes. Indeed, codependency between codons of overlapping protein-coding regions imposes a unique set of evolutionary constraints, making it a costly arrangement. Yet in cases of tightly coexpressed interacting proteins, dual coding may be advantageous. Here we show that although dual coding is nearly impossible by chance, a number of human transcripts contain overlapping coding regions. Using newly developed statistical techniques, we identified 40 candidate genes with evolutionarily conserved overlapping coding regions. Because our approach is conservative, we expect mammals to possess more dual-coding genes. Our results emphasize that the skepticism surrounding eukaryotic dual coding is unwarranted: rather than being artifacts, overlapping reading frames are often hallmarks of fascinating biology.

Coding of multiple proteins by overlapping reading frames is indeed an unexpected outcome of a selection process whose options are stochastically generated. The authors allude to the obvious when they observe that dual coding imposes constraints on amino acid possibilities. Note the following paragraph and its introductory headline (article quotes in blue). It contains some helpful definitions:

Dual Coding Is Virtually Impossible by Chance

Before describing our analyses, we define terms used in this paper. A dual-coding gene contains two frames read in the same direction: canonical (annotated as protein coding in literature and/or databases) and alternative. The alternative reading frame (ARF) is shifted forward one or two nucleotides relative to the canonical frame (+1 and +2 ARFs, respectively). To identify dual-coding genes, we used a comparative genomics strategy, because all presently known alternative reading frames are conserved in multiple species. For example, ARFs in Gnas1, XBP1, and INK4A are conserved in all sequenced mammals [8,10,12].

It is highly improbable that the encoding sequences for two distinct proteins would align exactly as required to confer function to both. The conclusion notes probability in deducing a likelihood of functionality.

Maintenance of dual-coding regions is evolutionarily costly and their occurrence by chance is statistically improbable. Therefore, an ARF that is conserved in multiple species is highly likely to be functional.


1 Center for Comparative Genomics and Bioinformatics, The Pennsylvania State University, University Park, Pennsylvania, United States of America, 2 Integrative Bioinformatics Institute, Vrije Universiteit, Amsterdam, The Netherlands, 3 Antiviral Research Center, University of California San Diego, La Jolla, California, United States of America

Günter Blobel

Cellular biologist Günter Blobel, M.D., Ph.D., was born on May 21, 1936 in Waltersdorf, Germany. In 1945 Blobel and his family fled their home in what was the eastern part of Germany to escape from the advancing Russian Red Army and settled in the town of Freiberg in East Germany. Günter Blobel graduated high school in 1954 and left Freiberg to settle in Frankfurt, West Germany after he had been denied access to a university education in East Germany.1

Blobel discovered a link between what is known as an SRM- signal recognition particle- and an organelle known as the endoplasmic reticulum. This helped establish what is called a cellular zip code system enabling the routing of up to a billion proteins within a cell to their proper locations. These routing locations include structures called organelles of which the endoplasmic reticulum is one.

"Each newly made protein has an organelle-specific address, a stretch of the protein referred to as a signal sequence that is recognized by receptors on an organelle's surface. Blobel and his colleagues also showed that, for at least one organelle called the endoplasmic reticulum, the binding of the signal sequence to its receptor opens a watery channel in the membrane through which the protein can travel."2

1. Günter Blobel The Nobel Prize in Physiology or Medicine 1999; http://nobelprize.org/nobel_prizes/medicine/laureates/1999/blobel-autobio.html

2. Rockefeller University News; http://www.rockefeller.edu/pubinfo/blobelbio.php

Other References:

3. Gunter Blobel, 1999 Nobel Prize Laureate in Physiology/Medicine and Pioneer in Protein Targeting Within/out of the Cell by Michael Vishnevetsky Midwood High School at Brooklyn College, Brooklyn; http://www.nyas.org/programs/nobel/essay3.html

Reactivating 'Week in Science'

The website Week in Science has resumed operations. Two new articles have appeared entitled Fill the Tank with Water Please and Bacterial Geometric Trails. Fill the Tank with Water tells of a potential promising new technology that could have us someday filling our lawnmowers and automobiles with water instead of gasoline. The fuel burned would be hydrogen and the exhaust water vapor. Very environmental friendly.

Bacterial Geometric Trails refers to a PNAS paper which notes some interesting movement patterns of a bacterial pathogen. The different patterns are mathematically defined and explained in terms of the operation of an underlying mechanism.

Confusing a Symbol with the Real Thing

Eric, a commenter at Telic Thoughts, has proven to be most resourceful at distinguishing between genuine and apparent supporting evidence. The following is taken from one of his comments and refers to the matter of self-replicating RNA.

"To illustrate, codons within DNA are free to encode for any sequence of amino acids because there are no chemical restrictions on the order of the base pairs in DNA. Do you intend to claim that the internal structure of RNA is similary free to be rearranged in any fashion (and still retain peer-replication ability)?

In any case, replication is inherently inadequate.

If the goal is to get to the moon, a hot air balloon cannot take you there.
If the goal is to traverse an ocean, a car cannot take you there.
If the goal is driving cross country, riding the Replication merry-go-round cannot take you there, no matter how long you ride.

The word "mountain" is not a mountain, and
a codon sequence in DNA is not an amino acid sequence for a functional protein, but
a replicated RNA molecule still gives you an RNA molecule.

RNA does not represent RNA. RNA is RNA.

A coded sequence of symbols represents something other than itself. If you want to travel cross country, you have to find a way off of the Replication merry-go-round."

Science is About Conflict not Consensus

A post at Viewpoint called 'Bad Science' reminds us of what science should be about. It should not be a search for accomodation or consensus. That can be left to politics. A spirit of challenge should be the scientific norm. Below is a quote from the linked post. It takes note that challenges are not always welcome.

"Science lives with internal conflict all the time," Olivero said. "Part of what we have to do is continually challenge each other."

That process, they say, leads scientists closer to truths that may be elusive for lifetimes.

I see. Science is about dissent and conflict, not consensus. Does this mean that the Darwinians on campuses all around the country who are demanding that non-Darwinians be silenced because they stand outside the scientific consensus are acting in a manner harmful to good science? Perhaps merely to ask the question is to answer it."

Around the Blogosphere 5/17/07

http://telicthoughts.com/id-101-2/

ID 101 by Mike Gene. It sets forth this question initially posed by William Dembski:

"Intelligent design begins with a seemingly innocuous question: Can objects, even if nothing is known about how they arose, exhibit features that reliably signal the action of an intelligent cause?"


http://telicthoughts.com/bits-and-pieces-of-an-rna-world/

Analyzing a paper about the RNA world.


http://telicthoughts.com/keep-the-thought-police-on-alert/

The denial of tenure to Guillermo Gonzalez


http://telicthoughts.com/a-question-of-style-guillermo-gonzalez-and-the-tenure-review-process/

Krauze on Ed Brayton's response to Gonzalez and the tenure issue.


http://www.evolutionnews.org/2007/05/guillermo_gonzalezs_denial_of.html#more

Darwinian intolerace comes to the surface.


http://post-darwinist.blogspot.com/2007/05/denied-tenure-habitable-zone-astronomer.html

Denyse O'Leary weighs in on the Gonzalez issue.


http://post-darwinist.blogspot.com/2007/05/thinkquote-of-day-did-einstein-believe.html

Einstein and intelligent design.


http://www.uncommondescent.com/evolution/endogenous-retroviruses-in-the-case-for-common-ancestry/

Case studies and arguments related to endogenous retroviruses.


http://www.uncommondescent.com/evolution/survival-of-the-rarest/

A twist on genetic fitness.


http://www.uncommondescent.com/intelligent-design/lets-hear-it-for-junk/

It's about what controls genes.


http://helives.blogspot.com/2007/05/dont-wait-to-be-cosmologist.html

David Heddle touches on cosmological ID.

Loops and Stretching

'Stretch a DNA Loop, Turn Off Proteins' reveals how the regulation of gene expression can be a consequence of the mechanical structure of DNA. Specifically discussed are loops, the stretching of DNA and proteins. A paragraph from the linked article:

"Biologists have discovered that the physical manifestation of DNA loops are a consequence of many biochemical processes in the cell, such as the regulation of gene expression. In other words, these loops indicate the presence of enzymes or other proteins that are turned on. Now physicists at the University of California, San Diego have discovered that stretching the DNA molecule can also turn off the proteins known to cause loops in DNA."

The Significance of Minimal Genome Concepts

'How many genes can make a cell: the minimal-gene-set concept' contains an abstract; a part of which follows. The abstract in full is linked.

"Several theoretical and experimental studies have endeavored to derive the minimal set of genes that are necessary and sufficient to sustain a functioning cell under ideal conditions, that is, in the presence of unlimited amounts of all essential nutrients and in the absence of any adverse factors, including competition. A comparison of the first two completed bacterial genomes, those of the parasites Haemophilus influenzae and Mycoplasma genitalium, produced a version of the minimal gene set consisting of approximately 250 genes. Very similar estimates were obtained by analyzing viable gene knockouts in Bacillus subtilis, M. genitalium, and Mycoplasma pneumoniae. With the accumulation and comparison of multiple complete genome sequences, it became clear that only approximately 80 genes of the 250 in the original minimal gene set are represented by orthologs in all life forms."

Despite multiple research projects, involving separate organisms, indicating minimal genome sizes that range up to several hundred genes, mainstream origin of life advocates have been scarcely influenced by implications derived from their results. OOLers continue to believe that pathways are amenable to paradigms envisioning continuous, small incremental changes. In my view the results of minimal genome studies lend strong support to a natural barrier concept. A minimal level of function, requiring a higher level of complexity than can be attained through continuous slight increments, fits a barrier model.

The response of OOLers is to claim that a precursor cell would have had different properties enabling a simpler replicating entity. Claims are easily made but where's the empircal evidence to back this one up?

Information

Recently an individual known as Eric has contributed some incisive commentary at Telic Thoughts. I've included some remarks from one of his comments in this blog entry. It concerns an exchange that touched on the topic of information within a thread that focused on the origin of life. Eric's comments are in blue.

Zachriel: Random noise *is* Shannon Information. There is more Shannon Information in a random sequence than in the text of Hamlet. …

Shannon Communiation doesn't require a coding algorithms.

But in a different note, you also wrote about "specified information". Just to be sure we are clear, I trust that you do realize and agree that random noise is never specified information, correct? And that a random sequence is an unspecified sequence, making "random" and "specified" mutually exclusive attributes, correct?

So, I am a bit surprised that you should separately ask "What odd definition of information are you using?" as though you hadn't referred to specified information or to coded information, or as though Shannon Information were the only possible meaning of "information".

I would have hoped that by now it would be plain that I am not talking vaguely about Shannon Information and especially not random noise. The context of my remarks was the genetic information that holds coded instructions for specifying amino acid sequences. This information is specified and it is in a code, which means that coding is required. Since you yourself have said

Zachriel: The genome is considered the coded information. The genome is decoded into proteins.

then I trust you shouldn't think it odd to refer to coded information, and I expect that everyone, including yourself, will agree that we should not expect to be able to decode random noise and get a functional protein. Its obviously not "odd" to refer to coded information with decodable, functional meaning.

Zachriel: We already know that genomes can evolve, creating new information in response to the environment.

is a question begging argument. Since the question is how unguided natural processes can create symbolic instructions that code for proteins in the first place, you can't appeal to an evolving, functional genome as any part of the explanation. That begs the question.

Well before the coded instructions in DNA can change through evolution, there must first be some coded instructions in DNA to begin with. My statement points out that you cannot get coded instructions for the creation of proteins out of DNA if you have never first encoded such instructions into DNA.

Neither does adding random noise provide a viable starting point. The fact that random noise might be counted as Shannon Information is irrelevant for the purposes of explaining the origin of coded information that can be decoded into proteins.

At this point I want to be careful not to attribute to you a position you do not hold, but I cannot help get the impression that you seem to hold that nature does not (ever?) encode from proteins to coded instructions. So I'd like you to please clarify this point.

If that were always true about nature, there would be no source for the intial protein instructions of the first genome, rendering it impossible to populate. That would make it impossible for a genome to get started by unguided natural processes. Hence my reference to "Game. Set. Match."

Mindless matter has no imagination and cannot creatively invent the coded instructions prior to the creation of proteins. It could not anticipate proteins. Nor could it start with random noise and evolve that into coded instructions for protein construction. A mindless process would necessarily be required to derive the coded specified amino acid sequence from the only available source for that information, namely by encoding the symbolic sequence from an actual amino acid sequence.

A Sad Saga

Both Telic Thoughts and Uncommon Descent featured posts about the denial of tenure by Iowa State University to Guillermo Gonzalez, an assistant professor. Gonzalez was known to believe in intelligent design. Here are some comments at the two sites:

http://telicthoughts.com/keep-the-thought-police-on-alert/#comment-103737

http://telicthoughts.com/keep-the-thought-police-on-alert/#comment-104069

http://telicthoughts.com/keep-the-thought-police-on-alert/#comment-104261

http://www.uncommondescent.com/intelligent-design/habitable-zone-astronomer-guillermo-gonzalez-denied-tenure/#comment-120923

About Protein Synthesis

Here is a worthwhile article about protein synthesis from BioSolutions. Here is a part of the post:

"Protein translation involves the transfer of information from the mRNA into a peptide, composed of amino acids. This process is mediated by the ribosome, with the adaptation of the RNA sequence into amino acids mediated by transfer RNA. Numerous initation and elongation factors also play a role.

Translation requires a lot of energy, with the hydrolysis of approximately 4 NTP --> NDP per amino acid added. (This includes the aminoacylation of the tRNA. Thus, gene expression is highly regulated to ensure that only proteins that are required are translated.

Translation involves 3 processes: initiation, elongation, and termination."

Transposons: No Longer the Maligned DNA Family Member

An evolution News & Views blog entry of Casey Luskin entitled 'Biologists Report Important Gene Regulation Function for Transposons' has a lesson to impart about rendering premature judgements based on prejudice inducing paradigms. From the linked blog entry:

"Transposons are a type of DNA which many Darwinists have written off as mere genetic junk. The pro-Darwin TalkOrigins archive tells us that transposons "can be thought of as intragenomic parasites." But don’t feel bad for the poor transposons — it looks like they might be looking at a new career as “the DNA formerly known as junk": biologists from Stanford and UC Santa Cruz are reporting that "'Junk' DNA Now Looks Like Powerful Regulator."

That type of "junk" is the transposon. As the press release about the study explains, "Large swaths of garbled human DNA once dismissed as junk appear to contain some valuable sections." The scientists report that in the past, they "had identified a handful of transposons that seemed to regulate nearby genes. However, it wasn't clear how common the phenomenon might be. 'Now we've shown that transposons may be a major vehicle for evolutionary novelty.'…" Taking off the "evolutionary" spin, the translation is: they think transposons play important roles in gene regulation."

Of course almost everything we observe in organisms is attributed to a selected genomic accident. There is no change here. However the rogue genomic elements concept has at least been adjusted with a story of subsequent taming.

"According to the press release, however, it has taken scientists decades to investigate and validate this function—a lot longer than it should have: "Bejerano and his colleagues aren't the first to suggest that transposons play a role in regulating nearby genes. In fact, Nobel laureate Barbara McClintock, PhD, who first discovered transposons, proposed in 1956 that they could help determine the timing for when nearby genes turn on and off."

Apparently this idea was stalled out due to the evolutionary assumption, á la Talk Origins, that they are nothing more than useless "intragenomic parasites." Yet it was as far back as 1990 that pro-ID scientist and Discovery Institute fellow Forrest Mims had warned in a letter to Science against assuming that "junk" DNA was "useless" (scroll to the bottom of the page to see the letter). Science wouldn't publish his letter, but it now appears that another prediction of intelligent design has been validated."

The refusal to publish the letter looks damning with hindsight. But why publish the views of one who bucks the tide of conventional thinking? Darwinists can be insufferably arrogant.

More on Haldane's Dilemna

A Bradford comment at Telic Thoughts serves as a useful device around which to frame this post. I had previously written this about Haldane's Dilemna and this about genetic load.

What does a deleterious mutation "look" like? It must impair without being lethal. The point has often been made that such mutations entail recessive alleles. But the implications of this are often misleading. When two recessive alleles are present and a deleterious mutation is expressed, impairment is observed. But death prior to reproduction is not a logical imperative. Let's get specific and examine a hearing impairment. Although the onset of the disease usually occurs before adulthood and hearing loss is progressive, one can survive and pass on his genes.

Mutations that impair but are not lethal are like nature's gene knockout experiments. Disable gene x and an organism loses the function correlating to it. However, such loss merely hinders an organism with respect to a function that may not be a vital one. But if there are non-vital functions then how do we know selection favored the gene in the first place? Because it confers an advantage, that when nullified by loss of function, results in no observable loss of reproductive capacity?

Mutations that compromise fitness, without being fatal, are common. They involve color blindness, speech defects, and a mutation that makes one more susceptible to addiction. There are also many, many other examples.

These types of mutations are well known. Also well known is the potential danger of a nuclear armed Iran. The common denominator of the two disparate facts may very well be a failure to draw correct conclusions based on data. Nature itself supplies case studies that are problematic for the idea that Haldane's Dilemna has been overcome. At least with respect to the concept that many theoretical beneficial mutations become fixed throughout a population.

Why are we to believe that genomic changes rendering slight advantages become fixed in populations? Why believe that specific identifiable genes, whose functions afford slight advantages, became fixed in accordance with standard theory, when affected organisms reproduce despite mutations causing loss of their function. Oh but the traits descendents of other more fit individuals will eventually become predominant right? But where are such perfect specimens in nature? In reality individual members of populations have slightly impaired functions of varying sorts. However solutions to Haldane's dilemna envision degrees of reproductive fitness centered on slight reproductive advantages which in reality are theoretical advantages that can become lost in the much bigger picture of many unaccounted for genomic pluses and minuses.

Chirality: Its cause and importance.

A chiral molecule is one that can exist as a pair of mirror image, non-super imposable enantiomers. This molecule requires a carbon atom that is attached to four different substituents (groups of atoms), the carbon is referred to as the stereogenic or chiral center. Methane (CH4) includes a carbon atom that is covalently bonded to four hydrogens. It contains no stereogenic center; therefore it is achiral. A carbon that is doubly bonded to another carbon (such as in an alkene) or to any atom (such as in ketones) are achiral by virtue of a carbon atom that is sp2 hybridized, the doubly bonded substituent would be counted twice. In ketones a carbon is doubly bonded to an oxygen molecule, this carbon would have at least two of the same substituents and therefore be achiral.

A mirror image, non-super imposable pair of enantiomeric molecules would be similar to a left hand/ right hand comparison. They look exactly the same but their three dimensional stereochemistry does not allow them to be super imposed on each other. Both pairs will have the same density, the same melting point and the same solubility the only difference being the direction to which they rotate polarized light.

Chirality plays a very important role in biological function. Since enantiomers do not have the same biological effect it’s important that the correct one is utilized; whether this is the construction of bio-macromolecules (proteins and nucleic acids) or the use of pharmaceutical drugs.

Dopamine has one stereogenic center; therefore exists in two pairs of enantiomers – levorotatory Dopa (L-Dopa. The ‘L’ signifies the counter clockwise direction that the asymmetrical molecule rotates polarized light) and dextrorotatory Dopa (D-Dopa – rotating polarized light clockwise). One enantiomer has no use biologically and the other fights Parkinson’s disease (L-Dopa). The L-enantiomer is the only stereoisomer that matches the target site’s chiral receptor. Like a ‘key in lock’ fit, the correct enantiomer is necessary in order to deliver the molecules biological benefit.

Historically in drug development and treatment, a racemic mixture of both enantiomers (50/50 mixture) would be used. It was simpler to yield a mixture opposed to just one of the enantiomers. But cases surfaced when the other enantiomer (not specific to the cure) did carry a negative effect. One instance would be the use of thalidomide to treat morning sickness in pregnant women. While the intended enantiomer performed its task, the other lead to deformities in babies.

The role of chirality and handedness in life’s origin is even more important. The incorrect enantiomer in drug design can harm life, the incorrect enantiomer in biological origins can prevent life. In order to obtain chiral molecules via synthesis you need to begin with a chiral starting material. Reactions between achiral reagents yield either racemic products (50/50) or meso-compounds (molecules with a stereogenic center but achiral by virtue of a symmetry plane that cuts through the molecule); neither of which are useful in constructing proteins or nucleic acids. Scientists have attempted to synthesize amino acids with the correct stereochemistry under the conditions that are believed to be similar to those of ancient Earth, but obtaining left-handed (L-enantiomer) dominance has proven elusive.

Even when considering an extraterrestrial source, such as the Murchison meteorite, no complete dominance in left-handed amino acids has been discovered. While some scientists noted a slight left-handed excess others stated that the amino acids were racemic and that any apparent dominance of left-handedness was from terrestrial contamination (Jeff Bada – Scripps Institute, Keith Kvenvolden – NASA Ames). There still exists some disagreement regarding the slight left-handed dominance or non-dominance in the meteorite, as well as over the sample being contaminated or uncontaminated; however, the possibility still remains that this meteorite may tell us nothing. There’s still a distance to travel from slight dominance to the degree of handedness that characterizes terrestrial life.

Around the Blogosphere 5/6/07

http://telicthoughts.com/john-wise-and-id/

A blog entry by Mike Gene examining part of an opinion piece by John Wise.


http://telicthoughts.com/hes-fine/

How to enlighten a panda.


http://www.uncommondescent.com/intelligent-design/the-challenges-that-materialist-atheism-cannot-face-effectively/

Denyse O'Leary's list of challenges to materialist atheism.


http://www.uncommondescent.com/education/darwin-dissed-by-doctors-but-a-design-revolution-continues-at-mit/

About Michael Egnor and the irrelevance of Darwinism to the practice of medicine.


http://post-darwinist.blogspot.com/2007/05/catholic-church-pope-benedict-on-design.html

The Pope on the universe, life and evidence for a creative intelligence.


http://www.evolutionnews.org/2007/05/time_what_michael_behe_actuall.html#more

'Time' magazine's failure to follow legitimate editing policies by substituting deceptive alterations of Behe in its place.


http://creationevolutiondesign.blogspot.com/2007/04/debate-over-creation-and-evolution-once.html

Globalization of the debate over creation and evolution.

A Response to Thought Provoker

A commenter at Telic Thoughts, who goes by the moniker Thought Provoker, asked me the following question:

"One of the reasons I pick on you so much with the "what is your proposal?" question is that you obviously know a lot about the subject. And rather than argue with you point by point, I am truly interested in understanding how you are making the logical connection needed for your holistic view. In other words, how does your Big Picture work even if all of your base assumptions are correct?"

My ID belief is that the universe and life on earth are a consequence of a cause having a purposeful and intelligent component. My base assumption is that intelligence and its associated purpose are detectable. Being a believer in the divinity of Christ, Christ would also be the designer in my view. However, that could not be established by fine tuning arguments or evidence that an initial genome was the product of an intelligently directed cause.

One of the purposes of this blog is to flesh out evidence for design as well as arguments for and against that view. I'm strongly sympathetic to the proposition that a minimally functional genome could not have arisen through a series of undirected steps. Such steps would need to generate incremental changes in nucleic acids in the direction of ever increasing information. Nothing we know about the chemical nature of nucleic acids or enzymatic proteins would lead us to believe a random series of chemical reactions would generate genomic information and an encoding convention through which the information would be expressed. To the contrary, functional cellular genomes come replete with intricate DNA repair mechanisms; indicating that the repair function is essential to maintaining genomic integrity. My position is that efficient repair would have been required at the outset. Consequently readers will observe a great deal of attention devoted to DNA repair at this blog.

It is also my view that a key component of evolutionary dynamics- natural selection- would not have been operational on a prebiotic earth. Natural selection is critical to countering design arguments. Darwin recognized this. It has been the single greatest weapon arrayed against Paley and all subsequent design positions.

Intelligent design has some interesting possibilities to elucidate ecological dynamics. Sub-optimal design, a counter-argument to intelligent design, often can be understood as a strategy to maintain a balance of nature. This paradigm appeals to the bigger picture and explains how too much efficiency or inefficiency, associated with individual species, can disrupt existing balances. I acknowledge, though, the need to devote more time to this aspect of ID.

I hope this answers some of your questions TP. TP has become a prolific commenter at Telic Thoughts.

Incidentally, we have added a new member to the team- Tim Lambert. I suspect some interesting blogs will be authored by him in the near future.

Check Out: 'Molecule of the Day'

'Molecule of the Day' is a good site for those having an interest in chemistry or those wishing to learn more about it. The linked blog entry is about nitrous acid and this paragraph from the post is useful to those of you having fish tanks:

"Its conjugate base is "nitrite," which is an important part of the nitrogen cycle in fish tanks - fish excrete ammonia, which bacteria oxidize to nitrite, which another set of bacteria oxidize to nitrate. Ammonia and nitrite are toxic, nitrate is (relatively) benign. You need a population of bacteria in your fish tank to oxidize ammonia and nitrite, otherwise you'll have sick-to-dead fish. This is why goldfish often die after a week (there also wasn't enough aeration or filtration) or why tanks get sick after the addition of too many fish - even healthy ones - at once."

Reverse Engineering in Biology

Reverse engineering is a term used with increasing frequency by intelligent design advocates. Michael Egnor wrote a blog entry at Evolution News & Views about bias at Wikepedia which referenced reverse engineering. This snippet is found in Egnor's linked post:

"I recently noted that the discovery of the structure and function of DNA was a good example of reverse engineering in biology and that the discovery of DNA had nothing to do with Darwin’s theory. Reverse engineering in biology is an inference to design, even if the inference is implicit and not explicit, and even if the scientist using the reverse engineering methodology doesn’t agree with the philosophical implications of the design inference. Much of modern molecular biology is the reverse engineering of biological molecules.

To illustrate my point, I linked to the "Reverse Engineering" entry in Wikipedia, which had a nice succinct definition:

Reverse engineering... is the process of discovering the technological principles of a device or object or system through analysis of its structure, function and operation…Reverse engineering is essentially science, using the scientific method. Sciences such as biology and physics can be seen as reverse engineering of biological 'machines' and the physical world respectively (emphasis mine). My post was published on Evolution News and Views on April 3rd.

On April 4th, the Wikipedia reference to biological reverse engineering was airbrushed out. It was changed to:

Reverse engineering … is the process of discovering the technological principles of a device or object or system through analysis of its structure, function and operation. It often involves taking something (e.g. a mechanical device, an electronic component, a software program) apart and analyzing its workings in detail, usually to try to make a new device or program that does the same thing without copying anything from the original. The verb form is to reverse engineer.

This was airbrushed:
Reverse engineering is essentially science, using the scientific method. Sciences such as biology and physics can be seen as reverse engineering of biological 'machines' and the physical world respectively"

There is an insecurity evident among too many opponents of intelligent design. It is not enough to dominate press coverage, major publications and academia. It is not enough to be able to present one's view and counter the views of the opposition in free societies. It is as if certain viewpoints must be quashed by self-appointed censors.

Wikepedia has been known to have its share of problems as this incident illustrates and ID critics are aware of its its lack of dependability. But imitating the airbrushers of a fallen empire should be beneath them.

Self-Replicators

This Bradford commment following a blog entry by Mike Gene at Telic Thoughts is the focal point for this post:

When you absorb information through the symbols you see on your computer screen you know the sender's pet cat or infant toddler cannot be implicated. That type of chance event is ruled out by probability. But what about selection? If a mutation in a unicellular organism can generate an adaptive response then why could a similar process not generate an initial genome? The reason lies in the properties of functional genomes. In contrast to "emergent properties" these ones are identifiable. Selection is linked to replication. If a self-replicating molecule is the object of study the only valid assumption that can be made, from a selection POV, is that changes disrupting replication will not be passed on. One cannot even assume that changes that make a replicator a more efficient one will be selected without knowledge of the supply of relevant nucleotides or AAs. A theoretical change that enhances efficiency might exhaust a natural supply source. In any case there is still no directional indicator pointing toward a cell. There is no theoretical support for von Neumann's insight when "information" and its replicating mechanism are one and the same. The type of materialist preconceptions represented by self-replicating molecules are inconsistent with what we actually observe. We observe encoding conventions and symbolic representations and accurately attribute their cause to intelligence. We are more justified in logically linking codes to intelligence than the materialist is in linking them to unknown forces of nature. The intelligence linkage needs to be the base assumption. When it is, ID arguments for an independence of reason from brain matter easily flow. Intelligence predates brains, stunney and the design you are looking for, bFast, is found in biology's first von Neumann transcriptor.

The point is made that natural selection indicates no directional flow to a self-replicating molecule model. For example, why should we assume selection directs an RNA self-replicator to a cell? Based on experimental evidence? Yet there is more to this. A self-replicating molecule is the wrong model. Cells are best described as having numerous biological sub-systems with different functions; each one having many molecules. Organized biological systems replicate. If von Neumann were to theorize about a self-replicating robot, having many interacting parts, why would he use a single nut or bolt around which to fashion a model? Why would he even use a computer chip if the chip contains no programming information and there are no protocols yet existing?