Wednesday, January 31, 2007

Dissing ID

Opponents of ID have an array of weaponry at their disposal unrelated to scientific evidence. One of them is scorn spawned by intellectual arrogance. Two blog entries, one by Mike Gene of Telic Thoughts and the other by William Dembski from Uncommon Descent illustrate the point. Gene's blog is a humorous response to raging fulminations. From the source inspiring the Telic Thoughts blog:

"Scientists tend to get angry when confronted by what they see as the
gross distortion of truth promulgated by Intelligent Designers. This
has come across badly in 'balanced' debates in the media. As was the
case with arguments over the MMR vaccine, the scientist when provoked can unwittingly appear to be a fulminating zealot. By contrast, many of the proponents of Intelligent Design (ID)) have contrived to appear to be in favour of free speach. Aren't those scientists empurpled with rage and crying "nonsense" the very picture of a threatened Establishment? On this platform the evolutionary scientist rather than the ID enthusiast can be seen the less reasonable of the two."

This illustrates the rage approach that attempts to depict IDers as untruthful because they advocate a position that mainstreamers are unable to refute.

Dembski's blog, J. Scott Turner in the Chronicle of Higher Education- ID is asking the right questions! contains a comment in reaction to an attempt to belittle IDers. The italicized quote is followed by the comment in bold.

“Their intellectual pedigree might be suspect, their thinking might be wrong, but at least they are asking an interesting question: What is the meaning of design of the living world?”

I keep having to remind myself that it takes intellectual pedigree beyond reproach to believe in a theory of origins that like alchemy lacks causal specificity (sound familiar WD?). And of course only an Untermensch would doubt that unguided natural forces are capable of generating sequentially ordered and functional nucleic acids on prebiotic earth. Don’t even bother to ask if any genetic information, fortuitously acquired, would survive environmental damage occassioned by natural forces in the absence of genomic repair mechanisms. If you start taking such issues seriously your intellectual pedigree will be challenged. Keep the faith.

The dissing tactic masks the bluff and bluster behind the opposition's case.


Monday, January 29, 2007

Selection Criteria

Natural selection's center stage role in discussions involving the origin of life, evolution and intelligent design make it imperative to be clear about what is referred to when the term is invoked. It will be invoked frequently at this blog in coming weeks. Therefore I thought it might be helpful to delineate some concepts and apply verbal handles which can be referenced in coming posts.

Natural selection can entail subtle differences in nuance when applied to origin of life explanations as opposed to an evolutionary process. Since complex systems of interacting biomolecular components are identified more frequently with already existing cells, theorized selective properties of hypothesized building blocks are often viewed differently. The selective value of particular biochemicals might be attributed to a chemical selection bias creating a greater likelihood that products of specified chemical reactions would be essential cellular components. Essential recipe ingredients are looked for before interactions are envisioned. Deterministic mechanisms are the focal point of selection.

Cellular selection tends to be more of the jigsaw variety. The selective value of a cellular component is analyzed within the context of its utility as a part of a larger multi-component mechanism. There need be no genomic bias in the direction of change toward a specific nucleic acid configuration; only a biologically reasonable possibility of generating the needed encoding configuration. That configuration tends to be linked to specific protein properties enabling interaction with other proteins.

In coming posts I intend to highlight the significance of differing selection criteria to different biological phenomenon.

Sunday, January 28, 2007

DNA Repair through Transfers

'DNA binding and nucleotide flipping by the human DNA repair protein AGT' is an article that appeared in Nature Structural & Molecular Biology over two years ago. However, the information in it is still relevant. The article discussed enzymes that play a role in repairing damaged DNA. Specifically mentioned were O 6-alkylguanine-DNA alkyltransferase (AGT), and O 6-methylguanine-DNA methyltransferase (MGMT). Alkylation damage is a well known phenomenon whose corrective action involves enzymes that transfer an alkyl group from a nucleotide to an enzymatic polypeptide chain. Methyl groups are likewise transferred by other enzymes found in multiple species. This particular article pointed out that DNA helix-turn-helix (HTH) motifs facilitated the binding of proteins.

DNA repair involves a multi-faceted complex of mechanisms and this article provides a glimpse into part of the story. DNA repair- your cells would be caught dead without it.


Saturday, January 27, 2007

Consciousness and Emergent Properties

Materialists argue that consciousness is an emergent property of matter. There are not many options available to those claiming that matter and energy is all there is. Joy, from Telic Thoughts, had this to say in response to another comment. Some of her remarks follow along with my comments about them. My comments are in bold type. Her remarks begin with a one sentence quote from another comment in the next paragraph. Joy's reaction is italicized.

Joy would have us believe that "nonlinearity" and "emergence" are just fancy words for "magic"

Keith, in the application to consciousness, these labels have specific meaning. Yes, non-linear science tackles self-organization of matter, complex systems, condensed matter, etc., and in physics attempts to define 'rules' (sort of sub-laws) governing the spontaneous emergence of such things from inadequate substrates. There is no law or minor rule of the universe named "Joy," yet here I am.

Joy being a living example of consciousness.

The definition of "emergent property" is a property (quantity or quality) that is not reducible to any properties or collection of properties of the substrate. Look it up, it's not hard. Irreducible to the substrate. Merely calling it "emergent" does not explain where it came from or how it operates beyond the inadequate substrate.

Joy points out how the term emergent property has been loosely bandied about, yet it has a constricting definition. The mere labeling of something by that term indicates a lack of explanatory utility; a point ably made by Joy.

You assume that if we added up the number of neurons and multiplied by the number of brain 'modules' dedicated to certain tasks of information processing, consciousness must 'emerge' as a matter of physical course. A lot of the AI guys who put a lot of funding into consciousness researches think the same thing, hoping to create a conscious computer one of these days. But it hasn't happened yet (that they've let any of us know about, anyway, and it would be a big deal) and isn't likely to happen, imo.


Friday, January 26, 2007

Around the Blogosphere 1/26/07

A post by Wedge on DNA repair mechanisms. I like this one.

This one sentence post by Mike Gene evoked a huge response.

Denyse O'Leary's take on a familiar obfuscation tactic.

Science literacy advances contrary to what you might be hearing.

Poetry in the Genetic Code?

Wednesday, January 24, 2007

Justice and PETA

At Telic Thoughts "defenders of science" are sometimes spoofed as was the case with this post. Special interest groups, which include animal rights activists, have been known for their hostility to certain scientific procedures. Yet they escape the wrath coming from the "defenders of science" which IDers so easily arouse. This TT post alludes to an organization known as PETA.

PETA is making news. Andrew Cook and Adria Hinkle, PETA employees, have been indicted on 21 counts of Cruelty to Animals. As reported at this link: "Police in Ahoskie, North Carolina arrested Cook and Hinkle on June 15, 2005 near a shopping-center dumpster, from which they recovered 18 dead pets in trash bags. Thirteen additional dead animals were recovered from the PETA-owned van in which they were traveling. Witnesses from the Bertie County (NC) Animal Shelter and the Ahoskie Animal Hospital later confirmed that the two PETA employees had collected animals earlier that day -- including puppies and kittens -- on the promise that PETA would find them adoptive homes."

Pathways to an Intelligent or Telic Inference

An interview of Nancy Pearcey was brought up in a previous post. I've included two more questions and answers from the interview in this post. Nancy breaks down and categorizes different approaches to ID. From the interview:

CS: So there's an intelligent cause behind the DNA?

NP: Right. There are three major areas where ID builds its case. One is the fine tuning of the universe, the many physical constants of the universe that seem to be so finely tuned to allow life to emerge. Fundamental constants like gravity and the electromagnetic force have to be so incredibly precise in their values — and there are so many of them — that it boggles the mind to think they are merely all "cosmic coincidences." It begins to look, then, like they have the value they do because someone intended it that way. This is so widely recognized by cosmologists today that "the God question" is now a very open discussion. The second area where ID scientists are developing positive evidence for design is Mike Behe's argument that many structures in the cell do not seem to be the kind of things that could come about by a gradual process.

Nancy Pearcey points to fine tuning as the basis upon which a case for ID can be made.

CS: Irreducible complexity?

NP: Yes, but the media tend to misstate the argument in terms of "it's too complex to have evolved." That's too simplistic. It's really a logical question about what kind of structures can be constructed in gradual steps and which structures have to be organized at the beginning. Is it an aggregate structure — like a pile of sand, which can be built up one piece at a time — or is it a complex structure, for which you need a blueprint from the beginning because all the parts interrelate? A kind of structure that can't be built up gradualistically. And the third area where ID is building its case is the argument from DNA and information theory; that is, where does complex biological information come from? Do natural causes as we know them produce information?

In singling out irreducible complexity Nancy Pearcey first discounts the popular cliche that ID signifies an argument based on "its too complex to have evolved." Actual arguments focus on both mechanisms for generating change and natural selection. Irreducible complexity calls into question the adaquacy of both of these orthodox pillars. Pathways to new complex structures and functions involve a series of incremental changes; all of which must have selective value. Changes must become predominant throughout a population.

There are subtle variations of ID positions that center around both the mechanism for change and natural selection. At Telic Thoughts Mike Gene, Krauze and others have championed a case for front loading. This takes advantage of the natural selection concept in an interesting way. Assume that in a line of descent (represented by x and y) a gene (or genes) were found in x having no reproductive enhancing properties. However the same gene located in y was both functional and essential. This would involve inheritance based on a front loaded capacity identified through a selection anomaly.

My own ID candidate is focused on Nancy Pearcy's last area; information rich DNA. The history of life on earth, according to standard models, envisions processes that incrementally enhance the information content of DNA from its RNA world inception. The directional arrow is clear but acquired information must be retained for this model to be plausible. A complex of factors threaten the integrity of genomes including radiation, chemical reactions and copying errors. Existing mechanisms would have had to evolve to neutralize their effects. The question is could they evolve or must they be front loaded to prevent the destruction of life at its outset? Indications that information loss exceeds gains, in the absence of DNA repair mechanisms, supports ID.

Monday, January 22, 2007

An Arctic Discovery

A National Geographic news story Bizarre New Form of Life Found in Arctic Ocean, Scientists Announce, tells of the discovery of a new group of marine algae in the Arctic Ocean. They were named picobiliphytes because of their very small size.

The article indicates the organisms may yield commercial benefits. Quoting from the article: "Phycobilipigments are also rich sources of protein, and they are used as a food source in aquaculture hatcheries... If the new picobiliphytes can be grown in sufficient quantities to provide such a nutrient source, he added, "they will really be valuable."

Psalm 66; Verses 5-7

Come and see what the Lord has done, how awesome his works in man's behalf!

He turned the sea into dry land, they passed through the waters on foot- come, let us rejoice in him.

He rules forever by his power, his eyes watch the nations- let not the rebellious rise up against him.

Sunday, January 21, 2007

Conflating Empircal Claims with Paley

Judge Jones, in his Kitzmiller ruling, relied in part on the views of theologian John Haught who argued that Behe's irreducible complexity concept was analogous to Paley's watchmaker argument. Haught used the analogy to argue that ID be considered religious. Paley's argument was philosophical and a logical argument for the existence of God. It was not an argument based on testing hypotheses. Unlike Behe and other IDers, empirical support for his belief was not Paley's principle concern.

Charles Strohmer's Conversation with author Nancy Pearcey Intelligent Design, Creationism, Evolution, is an interview of Nancy Pearcey. Two questions and the answers to them are provided.

"Charles Strohmer: Give us a thumbnail sketch of intelligent design.

Nancy Pearcey: A key element is the claim that God's design is empirically detectable. It says: let's look and see whether there are certain hallmarks or diagnostic traits of intelligence in nature itself. The evidence I find most persuasive is DNA. It has the kind of structure that's found in a language and is not produced by natural causes acting by chance. For example, when I took my little boy to the park, we found a large beech tree covered with graffiti. Even a seven-year-old knows that when you see a message — "George loves Wendy" — carved into a tree, it's not the result of some type of acid etching or other nature force. Information is always the product of an intelligent agent.

CS: Well, I'll skip the joke about whether George is smart about loving Wendy! Are you saying that the claim of ID is similar to Paley's watchmaker analogy?

NP: Yes, but my understanding is that the main difference would be that Paley spoke in terms of knowing the Designer's purpose. That left him open to the objection: how can we know the Designer's purpose, what's in His mind? So you may not yet know the purpose, or the rules, but you can at least know that something has been intelligently manufactured, because it has a particular structure that natural causes don't produce but that intelligent causes do produce."

Nancy has put her finger on critical differences between Paley's argument and ID. She cited as evidence what- a technological device? Nope. DNA. She referred to its encoding features and "certain hallmarks or diagnostic traits of intelligence." More importantly she alluded to causality and intelligence as a possible causal factor. Intelligent causality is a familar experience to rational, human minds. So why would a theologian or a judge ignore this in favor of a single minded focus on a half-baked analogy? The truth is ID critics have their own religious and metaphysical motives. In contending their opposition is all about science they deceive only themselves.

Saturday, January 20, 2007

More on Kitzmiller

The Evolution News & Views blog entry Law Review Article Agrees That Judge Jones Went Too Far reveals the views of Philip A. Italiano as noted in the Rutgers Journal of Law & Religion. The topic is the judicial wisdom of Judge Jones' decision in the Kitzmiller case concerning whether ID is science. Quoting:

"Perhaps there theoretically could exist a factual scenario in which the motives of those who write intelligent design into a public school science curriculum are nonreligious, and in which the only way for a court to ascertain whether the policy has the effect of an actual or perceived endorsement of religion is to determine whether intelligent design is or is not science. Kitzmiller was not such a case, however, and until that case arises, courts should strike down such policies on narrower grounds. The Kitzmiller court could have struck down Dover's policy under either the Lemon test's purpose prong or under the endorsement test without judging the scientific validity of intelligent design." 1

Quoting from a Supreme Court decison:

In the realm of constitutional law, especially, this Court has perceived the embarrassment which is likely to result from an attempt to formulate rules or decide questions beyond the necessities of the immediate issue. It has preferred to follow the method of a gradual approach to the general by a systematically guarded application and extension of constitutional principles to particular cases as they arise, rather than by out of hand attempts to establish general rules to which future cases must be fitted.

(Village of Euclid v. Ambler Realty Co., 272 U.S. 365, 397 (1926).)

Defenders of Judge Jones have argued that his foray into the science question was necessitated by a request that he so decide this issue. Was it? Could Judge Jones have disregarded such a request in order to guard "application and extension of constitutional principles to particular cases as they arise, rather than by out of hand attempts to establish general rules to which future cases must be fitted?" Would not a decision based on religious intent have better satisfied the guidelines laid down by Village of Euclid v. Ambler Realty Co.?

1. Phillip A. Italiano, Kitzmiller v. Dover Area School District: The First Judicial Test for Intelligent Design, 8 Rutgers Journal of Law & Religion 4, 46 (Fall, 2006)

Friday, January 19, 2007

Distinguishing Design from Accidental Events: Part Three

This is the third and last post related to an Uncommon Descent blog entry debunking some Talk Origins concepts. The UD blog contains powerful arguments against the outdated TO concepts which the reader can access at the link. I'll reproduce the Talk Origins claims and add to UD's referenced data. The UD post items are italicized.

The Talk Origins view of SINEs/Alu:

…current evidence suggests that only a very few Alu sequences are active sources of transcripts; perhaps transcription from most copies is inhibited by the chromosomal environment of the insertion

Further, the excellent health of individuals who lack particular Alu insertions supports the view that these insertions do not serve any important function in human physiology.

As UD indicates, contrary to TO claims, there are many identified SINES known to be functional. Alu sequences, unique to primates, also have been linked to functions.

Furthermore, there is a growing body of evidence that Alu (a SINE) sequences are involved in gene regulation, such as in enhancing and silencing gene activity, or can act as a receptor-binding site — this is surely a precedent for the functionality of other types of pseudogenes. Future studies on the one million Alu copies scattered in the human genome should reveal further regulatory functions of these elements.1

Assumptions underlying the Talk Origins view of endogenous retroviruses are illustrated in the following:

Endogenous retroviruses are molecular remnants of a past parasitic viral infection. Occasionally, copies of a retrovirus genome are found in its host’s genome, and these retroviral gene copies are called endogenous retroviral sequences. Essentially all of these endogenous retroviruses contain mutations that would disrupt the function of their genes, as would be expected if they inserted millions of years ago with no selective pressure to maintain the function of the genes.

The next reference is further evidence cautioning against the assumption of dysfunction.

"More than one million copies of the 300-bp Alu element are interspersed throughout the human genome, with up to 75% of all known genes having Alu insertions within their introns and/or UTRs. Transcribed Alu sequences can alter splicing patterns by generating new exons, but other impacts of intragenic Alu elements on their host RNA are largely unexplored. Recently, repeat elements present in the introns or 3'-UTRs of 15 human brain RNAs have been shown to be targets for multiple adenosine to inosine (A-to-I) editing. Using a statistical approach, we find that editing of transcripts with embedded Alu sequences is a global phenomenon in the human transcriptome, observed in 2674 (2%) of all publicly available full-length human cDNAs (n = 128,406), from >250 libraries and >30 tissue sources. In the vast majority of edited RNAs, A-to-I substitutions are clustered within transcribed sense or antisense Alu sequences. Edited bases are primarily associated with retained introns, extended UTRs, or with transcripts that have no corresponding known gene. Therefore, Alu-associated RNA editing may be a mechanism for marking nonstandard transcripts, not destined for translation."2

More Of UD's reference to Talk Origins claims:

Talk Origins has this to say of LINES:
LINEs thus have several properties expected of “selfish” DNA sequences that can spread in the host DNA simply because they encode their own machinery for spreading.

In other words, they don’t serve a purpose other than to copy themselves, according to Talk Origins.

UD proceeds to document quite a few functions attributed to LINES. UD touches on an area of special interest to me in the mention that LINE-1s are able to integrate themselves into DNA lesions "resulting in retrotransposon-mediated DNA repair in mammalian cells."

Discussed also was a topic of central interest to endogenous retroviruses namely, whether or not they are evidence for common descent. The argument associated with this is based on the belief that their insertions are random and that markers found within corresponding genes of different species would be the result of shared errors.

This linked study shows the need for caution in assuming that SINE insertions indicate common ancestry. From the cited paper:

"Vertebrate retrotransposons have been used extensively for phylogenetic analyses and studies of molecular evolution. Information can be obtained from specific inserts either by comparing sequence differences that have accumulated over time in orthologous copies of that insert or by determining the presence or absence of that specific element at a particular site. The presence of specific copies has been deemed to be an essentially homoplasy-free phylogenetic character because the probability of multiple independent insertions into any one site has been believed to be nil. Mys elements are a type of LTR-containing retrotransposon present in Sigmodontine rodents. In this study we have shown that one particular insert, mys-9, is an extremely old insert present in multiple species of the genus Peromyscus. We have found that different copies of this insert show a surprising range of sizes, due primarily to a continuing series of SINE (short interspersed element) insertions into this locus. We have identified two hot spots for SINE insertion within mys-9 and at each hot spot have found that two independent SINE insertions have occurred at identical sites. These results have major repercussions for phylogenetic analyses based on SINE insertions, indicating the need for caution when one concludes that the existence of a SINE at a specific locus in multiple individuals is indicative of common ancestry. Although independent insertions at the same locus may be rare, SINE insertions are not homoplasy-free phylogenetic markers."3

One more item needs to be addressed which is relevant to inferences drawn from endogenous retroviruses. The origin of viruses themselves have a bearing on theories about endogenous retroviruses. Much of the data ciited in the UD post as well as this one support the theory that viruses have a sub-cellular origin. That is they would have have had some sort of cellular function and would have become independent of cells at some point except for their host dependency. This dependency, as well as the accumulating evidence for endogenous retrovirus function, would support the belief related to their sub-cellular origin.

1. 'Pseudogenes: Are They Non-Functional?'; by Pierre Jerlström; First published in Creation Ex Nihilo Technical Journal 14(3):15, 2000;

2. 'Widespread RNA Editing of Embedded Alu Elements in the Human Transcriptome';
Dennis D.Y. Kim1, Thomas T.Y. Kim, Thomas Walsh, Yoshifumi Kobayashi1, Tara C. Matise, Steven Buyske, and Abram Gabriel1; Genome Research 14:1719-1725, 2004;

3. 'An Ancient Retrovirus-like Element Contains Hot Spots for SINE Insertion'; Michael A. Cantrella, Brian J. Filanoski1, Angela R. Ingermann, Katherine Olssona, Nicole DiLuglioa, Zach Listera, and Holly A. Wichmana; Genetics, Vol. 158, 769-777, June 2001;

Wednesday, January 17, 2007

Around the Blogosphere 1/17/07

William's comment in reaction to a previous comment that "teaching evolutionary theory has a secular purpose, and it doesn't foster an excessive gov't entanglement with religion." William's mention of genomic repair mechanisms and this question: would you argue for suppression of teaching that references the concept (DNA repair mechanisms) and how does any of this entangle the government with religion?" brought about a strange response from another commentator.

Uncommon Descent's 'Every day biology is looking more and more designed'

Mesk (not an IDer) made this comment and more at Telic Thoughts:

"IDists need to approach things in this sort of way:

(1) Identify the evidence around them that constrains the possibility space of how the designer(s) may have acted;
(2) Use this evidence to generate explicit models incorporating the nature, motivations and design processes of the designer(s);
(3) Use these models to generate testable hypotheses about the world;
(4) Perform experiments and make observations in order to further constrain the possibility space and place further constraints on your models of the designer."

From TTer Steve Petermann:

"Then even if one finally gets to the so called four fundmental forces the question still remains. There is an infinite regress. Paul Davies points out this problem with his turtles example in this presentation where eventually there is a pissing contest on who's uber-turtle is the best.

It would seem that for those who insist that the designer must be independently known or know who or what designed the designer, they are also hamstringing science. In fact, as ID does, science tries to induce the characteristics of the fundamental causes from observations(that are not those fundamentals themselves)."

'Tandem Repeats, Growth and Form, Cellular Zip Codes, and Molecular Tags'

From Creation Evolution Headlines

'The Evolution of Electrical Engineering'

"Nerves carry electrical impulses. Ipso facto, they are subject to laws of physics concerning conductance, capacitance, and resistance. Getting a signal from one end of an animal to the other in time can be a matter of life and death. In order to maintain optimum levels of electrical conductivity to meet their lifestyle requirements, animals possess numerous adaptations to increase throughput. In a paper in Current Biology,1 D. K. Hartline (U of Hawaii) and D. R. Colman (McGill U, Quebec) described how these adaptations fall into two main categories: (more at the linked site)

Tuesday, January 16, 2007

Distinguishing Design from Accidental Events: Part Two

Uncommon Descent featured this post debunking some Talk Origins concepts. A continuation of comments on the UD post- quoting Shauer’s Article:

"They [transposons] are Necessary for Embryonic Development

The research, published in the October issue of Developmental Cell, suggests that retrotransposons may not be just the “junk DNA” once thought, but rather appear to be a large repository of start sites for initiating gene expression. Therefore, more than one third of the mouse and human genomes, previously thought to be nonfunctional, may play some role in the regulation of gene expression and promotion of genetic diversity. Dr. Barbara B. Knowles and colleagues from The Jackson Laboratory in Bar Harbor, Maine, found that distinct retrotransposon types are unexpectedly active in mouse eggs, and others are activated in early embryos. Surprisingly, by acting as alternative promoters, retrotransposon-derived controlling elements drive the coordinated expression of multiple mouse genes. The researchers think that expression of retrotransposons during very early stages may contribute to the reprogramming of the mammalian embryonic genome, a prerequisite for normal development."

Indeed, endogenous retroviruses can be connected with function, specific ones involving the developmental stages of mammals. "Syncytins, products of the env gene of HERV-W and HERV-FRD, contribute to human placenta development. Similar genes are also found in mouse and sheep. Indeed, the sheep ERV genes have been shown essential for sheep reproduction. Furthermore, regulation of the human syncytin-1 gene involves a complex regulation network including both viral and host factors."1

In addition, Endogenous retroviruses regulate periimplantation placental growth and differentiation reports the following:

"Endogenous retroviruses (ERVs) are fixed and abundant in the genomes of vertebrates. Circumstantial evidence suggests that ERVs play a role in mammalian reproduction, particularly placental morphogenesis, because intact ERV envelope genes were found to be expressed in the syncytiotrophoblasts of human and mouse placenta and to elicit fusion of cells in vitro. We report here in vivo and in vitro experiments finding that the envelope of a particular class of ERVs of sheep, endogenous Jaagsiekte sheep retroviruses (enJSRVs), regulates trophectoderm growth and differentiation in the periimplantation conceptus (embryo/fetus and associated extraembryonic membranes). The enJSRV envelope gene is expressed in the trophectoderm of the elongating ovine conceptus after day 12 of pregnancy. Loss-of-function experiments were conducted in utero by injecting morpholino antisense oligonucleotides on day 8 of pregnancy that blocked enJSRV envelope protein production in the conceptus trophectoderm. This approach retarded trophectoderm outgrowth during conceptus elongation and inhibited trophoblast giant binucleate cell differentiation as observed on day 16. Pregnancy loss was observed by day 20 in sheep receiving morpholino antisense oligonucleotides. In vitro inhibition of the enJSRV envelope reduced the proliferation of mononuclear trophectoderm cells isolated from day 15 conceptuses. Consequently, these results demonstrate that the enJSRV envelope regulates trophectoderm growth and differentiation in the periimplantation ovine conceptus. This work supports the hypothesis that ERVs play fundamental roles in placental morphogenesis and mammalian reproduction."2

If transposons insert fairly randomly as TalkOrigins claims, then that which preceeded a random insertion affecting embryonic development is most interesting. How did sheep reproduce prior to this putative random event? Was it a random event?


1. 'Were Retroviruses Created Good?'; by Dr. Yingguang Liu;

2. 'Endogenous retroviruses regulate periimplantation placental growth and differentiation'; PNAS | September 26, 2006 | vol. 103 | no. 39 | 14390-14395; Kathrin A. Dunlap, Massimo Palmarini, Mariana Varela, Robert C. Burghardt, Kanako Hayashi, Jennifer L. Farmer, and Thomas E. Spencer

Monday, January 15, 2007


Z-DNA-forming sequences generate large-scale deletions in mammalian cells tells of a condition that is associated with increased likelihood of genetic instability and incurrence of specific diseases. The condition- spontaneous chromosomal breakages- has been known to occur with greater frequency in genomic hot spots. These chromosomal breakpoints in turn are frequently found near Z-DNA forming sequences.

"There are three major structural forms of DNA; the B form, described by Watson and Crick in 1953, the A form and the Z form... Z-DNA is a left-handed helix that contains about twelve base pairs per turn... Transitions between the helical forms of DNA may play an important role in regulating gene expression."1

In mammalian cells, the Z-DNA-forming sequences induce double-strand breaks nearby, resulting in large-scale deletions in 95% of the mutants... Our data suggest that Z-DNA-forming sequences may be causative factors for gene translocations found in leukemias and lymphomas and that certain cellular conditions such as active transcription may increase the risk of Z-DNA-related genetic instability... Chromosomal translocations leading to carcinogenesis may be associated with normal metabolic processes as well as DNA damage caused by endogenous or environmental genotoxic agents.

The article notes that homologous recombination, which can lead to DNA repair, is induced by the formation of Z-DNA. It also indicates a conclusion that processing of Z-DNA by repair mechanisms in mammals can incur large-scale genomic rearrangements and deletions. A general theme of this blog is highlighting the central importance of DNA repair to the viability of life. DNA repair is varied and extensive. Z-DNA is another chapter of the story.


1. Biochemistry 3rd edition; Pamela C. Champe, Richard A. Harvey and Denise R. Ferrier; Lippencott Williams & Wilkins; Page 396.

2. Z-DNA-forming sequences generate large-scale deletions in mammalian cells; PNAS | February 21, 2006 | vol. 103 | no. 8 | 2677-2682; Guliang Wang, Laura A. Christensen, and Karen M. Vasquez


Sunday, January 14, 2007

Distinguishing Design from Accidental Events: Part One

Uncommon Descent featured this post which debunks some Talk Origins concepts. Among them is the TO view of tandem repeats. TO is quoted as stating that "scientists view tandem repeat sequences as resulting from accidental DNA duplications.” Then the actual roles of tandem repeats are laid out. They include silencing and activating genes. Tandom repeats are associated with specific promoters. They are linked to the lengths of dog noses and the percentage of fat in cow's milk. Tandom repeats are also believed to be a causal factor in determining the appearance of individuals; traits like amount of body fat, height, skin color and more. In fact, tandom repeats are so individually unique that they function like molecular fingerprints.

Does all this appear to result from "accidental DNA duplications?" If it does and tandem repeats influence such properties as body fat, milk fat, nose length, height, skin color and more then what determined these properties prior to these accidents? If you are familiar with the respective views of intelligent design advocates and the mainstream evolutionary community, then you know that the latter will explain any set of outcomes as consistent with their views. If tandem repeats were found to confer no functional utility then the associated explanation would be "what would you expect of accidental duplications?" If function is found then that too can be explained by random, selected changes. Tails I win, heads I win too.

What does TO have to say about transposons? As quoted by UD:

"In many ways, transposons are very similar to viruses. However, they lack genes for viral coat proteins, cannot cross cellular boundaries, and thus they replicate only in the genome of their host. They can be thought of as intragenomic parasites.…finding the same transposon in the same chromosomal location in two different organisms is strong direct evidence of common ancestry, since they insert fairly randomly and generally cannot be transmitted except by inheritance…."

A good set up argument for common ancestry but there is more to this. Fairly random insertion is dubious as this linked study indicates. "Analysis of in vivo integration patterns has provided no data to support the notion that retroelement integration is random. Rather, the diversity of insertion patterns of retroelements suggests numerous ways in which genomic DNA is identified for preferential targeting."1

And there is this: "Retrotransposon and retroviral insertions are not randomly distributed on chromosomes, suggesting that retroelements actively select integration sites. This is the case for the yeast Ty5 retrotransposons, which preferentially integrate into domains of silent chromatin at the HM loci and telomeres."2

1. PubMed; 'Integration specificity of retrotransposons and retroviruses;' Sandmeyer SB, Hansen LJ, Chalker DL.

2. Genes & Development; Vol. 13, No. 20, pp. 2738-2749, October 15, 1999;
'Tagging chromatin with retrotransposons: target specificity of the Saccharomyces Ty5 retrotransposon changes with the chromosomal localization of Sir3p and Sir4p;'
Yunxia Zhu, Sige Zou, David A. Wright, and Daniel F. Voytas

Friday, January 12, 2007

Justice from the Perspective of a Child Rapist

Bill O'Reilly covered a story tonight on his program 'The O'Reilly Factor' which told of a case in Vermont in which an admitted child rapist was placed on probation rather than given jail time. This is not a reference to the previous story referred to below involving Judge Cashman. Rather, this is another incident about which we will undoubtedly hear much more in days to come. Although we cover stories related to intelligent design, evolution, abiogenesis etc. I'm going to devote some attention to this for good reasons.

First, the offense itself is as repugnant as they come. It is an assault on the most defenseless and innocent among us and merits attention. Second, all of us have a stake in a morally responsible judicial system. The judiciary is more isolated from public opinion than the other branches of government and for good reasons. But it needs to be held accountable to standards of common decency. Our judicial system impacts all areas of life. When outcries against blatent abuse are muted you can rest assured that injustice, incidental to lower profile cases, will be evermore problematic. The following quote, which is intended to refresh some memories and inform others, was obtained from the linked website:

"The story began with a tragic case of sexual abuse and seemingly ended with a guilty plea in a Vermont courtroom. Thirty-seven-year old Mark Hulett pled guilty to aggravated sexual assault on his close friend's daughter. The attacks occured from the time she was six years old until she turned ten. In front of Judge Edward Cashman, prosecutor Nicole Andreson asked that Hulett be sentenced to 8-20 years in prison, but on January 4th, Judge Cashman surprised everyone there by sentencing him to only 60 days in jail and ordered him to complete sex offender treatment after his release. At the hearing, Cashman explained, "...[punishment] accomplishes nothing of value... and it costs us a lot of money." Hulett will be out in 2 months."

I've witnessed arguments from authority in previous encounters with attorneys. If you realized that... Oddly enough this does not go both ways. Critics unable to distinguish between 'The O'Reilly Factor' and a transcription factor are not hesitant to air their views about ID. I would hope that if the story reported by O'Reilly is accurate, we'll see some outrage from the legal community.

Bullet News

* From 'Nature Structural & Molecular Biology' an article, (Heme is involved in microRNA processing) about microRNAs (miRNAs) and how their regulating functions impact the expression of protein-coding genes.

* From ( astro-ph/0610377) an article addressing the question of whether intelligent life exists elsewhere in the universe. If you are interested in this field this article has some details about detection issues.

* Do pileated woodpeckers get headaches? After all they hammer their heads into trees with great force.

"During courtship, male woodpeckers will drum up to 12,000 times a day," he said. "If they were to say to their mates, 'Not tonight, honey, I've got a headache,' woodpeckers wouldn't advance."

Not an excuse for a woodpecker.

Thursday, January 11, 2007

The Limits of Darwinian Pathways

Intelligent design is a science, not a faith makes the case that: "If certain Darwinists also had the intellectual honesty to distinguish between science and their religious beliefs, the public understanding of science would be much enhanced." That would come as a revelation to those who believe their views of natural history flow from scientific inferences rather than a combination of scientific data and their own subjective viewpoints. From the article:

"If Darwin had known what we now know about molecular biology - gigabytes of coded information in DNA, cells rife with tiny machines, the highly specific structures of certain proteins - would he have found his own theory convincing? Randerson thinks that natural selection works fine to explain the origin of molecular machines. But the fact is that we are still unable even to guess Darwinian pathways for the origin of most complex biological structures.

Science has turned lots of corners since Darwin, and many of them have thrown up data quite unpredicted by his theory. Who, on Darwinian premises, would have expected that the patterns of distribution and abundance of species in tropical rainforests could be modelled without taking local adaptation into account? Or that whenever we sequence a new genome we find unique genes, unlike any found in other species? Or that bacteria gain pathogenicity (the ability to cause disease) by losing genes?"

Intelligent design advocates need to align solid empirical data in support of theory. It is a new and developing field. But they are working at it in spite of their detractors. If the foregoing sounds familiar then perhaps you too have been reading comments made by mainstream defenders of origin of life beliefs. Those "gigabytes of coded information in DNA" have resisted efforts by the mainstream scientific community to account for their origins. It's time to look elsewhere.

Wednesday, January 10, 2007

Around the Blogosphere 1/10/07

Salvador Cordova's comment referencing a link to an Uncommon Descent blog entry. It cites a peer-reviewed article by Trevors and Abel and recognition of some IDers.

Mike Gene's post 'Sophisticated RNA' This from the post:

"The non-teleological perspective views RNA as a primitive, ancient relic of the process of abiogenesis. The teleological perspective views RNA as a sophisticated molecule that plays an essential control function within the cell and has never existed apart from its cellular context."

Me and ID by Mike Gene. His views on a number of topics.

Design principles and the ear.

A post on Alvin Plantinga's review of Dawkins' book 'The God Delusion.'

"The secret handshake"- some humor by Dave Scott.

'Einstein's Greatest Mistake' Evidence for an intelligently designed universe.

Sunday, January 07, 2007

Junk DNA not so junk after all

We used to be told that there were around 100 vestigial organs in the human body, supposedly the result of evolution. A hundred years later, the list is down to zero. (Curiously, there were never any reports of nascent organs, that did not yet have a function but were going to get there one day.) Nowadays, we hear a great deal about "junk DNA". Just like their Victorian predecessors, the evolutionists arrogantly assume that anything they don't understand is useless junk. Then they use their arrogant assumption as "evidence" for evolution.

A link on Creation-Evolution News led me to this summary of research results showing that many bits of supposed junk DNA actually have a purpose.

If we approach the DNA with the assumption that it was created, we will be better placed to discover all the functionality that must be hidden in it. Here as in so many other places, evolutionism is a blind alley.

For you formed my inmost being.
You knit me together in my mother’s womb.
I will give thanks to you,
For I am fearfully and wonderfully made.
Your works are wonderful.
My soul knows that very well. (Ps 139:13-14)

What's behind the hate speech?

I recently joined the Yahoo group, EvolutionGroup, and I've been struck afresh by how virulent the attitudes of evolutionists are towards anyone who questions their view of the world. It seems they will habitually accuse their opponents of lying and incompetence. No matter what evidence is being presented against their ideas, some of them will, almost without fail, descend to ad hominem attacks. In fact, the better the evidence, the more virulent they become.

They seem to be quite incapable of taking part in a reasoned debate about this subject.

I believe that the reason for this is spiritual and that what seems frankly irrational behaviour can be understood when spiritual things are taken into account.

As a biblical Christian, I have a prior commitment to the bible as the inspired and inerrant word of God. As far as I am concerned, the existence of God and the inerrancy of the bible are two basic axioms that should inform all human reasoning, in science as in everything else. (I don't, therefore, have a great deal of sympathy for pure ID, which claims not to make any assumptions about the creator; but at least it is not totally blinkered by naturalism.)

When we use the bible to explain what is happening, a lot of things become clearer. Almost at the very beginning we see our enemy and God's deceiving Eve and enticing our first parents away from God. As a result of that sin, Adam somehow handed over authority to Satan, so that Paul calls him the "god of this world" who has "blinded the minds of the unbelieving" (2 Cor 4:4). It is clear that Satan has power over unbelievers to deceive them: he is called "a liar and the father of lies" (John 8:44). Jesus also calls him "a murderer from the beginning" (ibid). In Genesis we saw Satan as the serpent, the deceiver. In Revelation we see him as the dragon, the murderer. These are the basic elements of his character.

As deceiver, Satan has been very successful over the past 300 years in turning men away from the bible to believe in fantasies of their own—as they think—but really of his making. Multitudes have been turned from faith because they believed the lie of evolution. This should not be a great surprise to us. Evolutionary ideas have actually been around for thousands of years and are bound to be attractive since they allow people to think they can deny God's rule over the world. The difference with Darwinism was that it provided a pseudo-scientific mechanism by which evolution could supposedly happen. Along with this goes the hijacking of science by naturalism, claiming that even the possibility of divine action should be excluded from science. The creation science movement, and ID too, are attempting to expose these lies. If they succeed, they will derail Satan's efforts to turn the whole world away from God. This explains the extraordinary virulence of evolutionists against us. Since (like all unbelievers) they belong, by nature, to the devil (1 John 3:8), they are his tools and to some extent express his character.

Do not be surprised, then, when Dawkins and his like indulge in hate speech against Christians, especially creationist ones, and accuse ID writers of incompetence and dishonesty. They are merely serving as their master's mouthpieces, though they do not (I hope) know it. Christians need to realise that this is not just a debate about science, but is a battle in the heavenly places that will ultimately be won not by reasoned argument, for our opponents mostly do not listen to reason, but by prayer and the word of God.

For though we walk in the flesh, we don’t wage war according to the flesh; for the weapons of our warfare are not of the flesh, but mighty before God to the throwing down of strongholds, throwing down imaginations and every high thing that is exalted against the knowledge of God, and bringing every thought into captivity to the obedience of Christ; and being in readiness to avenge all disobedience, when your obedience will be made full. (2 Cor 10:3-6)

It Comes Down to Intuition?

Uncommon Descent features a post on the emerald cockroach wasp which provoked some opinionated responses from commentators. The emerald cockroach wasp administers a double sting to a roach which modifies its behavoir allowing the wasp to drive it to its den. There wasp larva are able to use it as a source of nourishment. The evolution of the capacities enabling the wasp to accomplish this are termed an imaginary story and many comments follow.

Many of the comments fall into one of two categories. Those which debunk evolution of this creature as fanciful and those which debunk God as fanciful. It is a commonly observed pattern in ID vs. evolution exchanges. URLs to some sample comments:

Note the exchanges of statements of incredulity. Both sides unable to find the other side credible. My favorites are the last two; the second to last a standard evolutionist and the last an IDer. There is some unusual candor on display. Dispensed with is the fiction that it's all about objective analysis of data. Substituted explanations include the mention of intuition.

Interestingly, some anti-IDers seem to acknowledge the plausibility of a design inference on the one hand while focusing their personal incredulity on the possibility of God. It is saying, in effect, that ID is not an option because inferences based on it are unbelievable.

Professor Kenneth Miller popularized the term "argument from personal incredulity." It is generally invoked by critics of ID at junctures where theoretical constructs are weak (origins) or particular models have problems. It alleges that disbelievers are basing their disbeliefs on their personal subjective assessments rather than the data. If the people involved in this particular debate, or the larger one that encompasses it, are grouped according to their metaphysical perferences, you will find that those believing in God might be mainstreamers, modified mainstreamers or opposed to existing explanations. There is variety among them.

On the other hand those whose metaphysics excludes divine possibilites almost always opt for standard explanations up and down the line including abiogenesis. There is little variation among them. So then, which side expresses views dictated by their personal subjective assessments?

Saturday, January 06, 2007

New Links

I've added two new links to the site. Desafiando a Nomenklatura Cientifica is a blog writen in Portuguese. If you are able to read the language give this blog a look.

Boston 1775 is focused on American history; particularly that part of it relevant to the American Revolution. If you are involved with your kids and their homework or if you just like American history, this site is a good one.

Finally a post from the Yahoo group, Intelligently Sequenced, that refers to a news item of interest to creationists, IDers and evolutionists.

Odd Couple

Unusual relationships? Check this one out. There are silver linings even with natural disasters.


Friday, January 05, 2007

What Clues Indicate a Planet is Livable?

The article, 'Earth: The Lone Pale Blue Dot?' details specific indicators that another planet could harbor life. Searching for extra-terrestrial life would be an important mission for future space expeditions. So what are the clues that a planet could be hospitable to life? The answer from this NASA site:

"To determine if a planet is livable, scientists will look for carbon dioxide and water vapor, signposts that a planet has an atmosphere and oceans, respectively. Atmospheres not only provide air to breathe, but also act like blankets to keep a planet warm and help buffer potential residents from damaging ultraviolet and cosmic rays. Oceans help regulate a planet's temperature and provide liquid water, an essential ingredient for life on Earth."

It is believed that some molecules indicate life already exists. Oxygen, ozone and methane would suggest this. Methane is associated with swamps on earth and oxygen is expelled by plants on this planet. However detection of molecules like these can also be false positives for life. Saturn's moon Titan has an atmosphere containing methane but no living organisms.

Between oxygen and methane the former is the better indicator of life but both found together would be very convincing according to Dr. Victoria Meadows of NASA's Spitzer Science Center, in Pasadena, California. Dr. Meadows said, "for example, if we found carbon dioxide, oxygen and water vapor, in addition to methane, then we'd be pretty convinced that we were looking at an environment like our own."

Molecules can also indicate an environment that is hostile to life. Sulfur dioxide is an example and suggests a dead planet.

Thursday, January 04, 2007

The Designer's Recipe

This brief essay, DNA: A Stew-pendous Creation by Frank Sherwin, M.A., is a reminder that the facts of nature do not conflict with creation. Because we can refer to specifics like DNA and give rational reasons why DNA is better explained by non-standard analyses than the RNA world, we have data for intelligent design as well. I am a Christian but I do not need scriptural references to support a solid case for origins by design. Mindful of some recent comments I have included much of the essay but have left out footnotes and other information that can be read at the linked site. The essay follows. My comments are in bold.

"Often those who prefer non-Darwinian explanations for the origin of the species are accused of being unscientific. One may believe in creation (or intelligent design), evolutionists maintain, but there certainly isn't any evidence for it. Ironically, it is research by the scientific community that begs to differ, revealing stunning and sophisticated features of the living world:

DNA's simple and elegant structure -- the "twisted ladder," with sugar-phosphate chains making up the "rails" and oxygen- and nitrogen-containing chemical "rungs" tenuously uniting the two halves -- seems to be the work of an accomplished sculptor.

Yet the graceful, sinuous profile of the DNA double helix is the result of random chemical reactions in a simmering, primordial stew. Just how nature arrived at this molecule and its sister molecule, RNA, remains one of the greatest -- and potentially unsolvable -- scientific mysteries."1

There are a number of points of note in this remarkable quote. The most obvious is that judging simply by what the secular scientist can see (Romans 1:20), DNA has all the earmarks of a Sculptor who is gifted, skilled, and clever. But then notice they deny what is "clearly seen" choosing to attribute the "graceful, sinuous profile" of DNA to "a simmering, primordial stew." In 1952 a graduate student in Chicago attempted to emulate prebiotic conditions on a young Earth "billions of years ago." But organic life and DNA were never "created."2 What biochemists cannot do given almost unlimited funding, time, and contact with the brightest and best scientific minds in the world -- a "simmering, primordial stew" can do! There have been other simulation experiments, but no one has been able to make "the sugar molecules dioxy-ribose |sic| and ribose necessary to build DNA and RNA molecules."3

Besides having "the earmarks of a sculptor" DNA also has encoding features associated with an intelligent and gifted programmer and some related translating mechanisms worthy of a linguist. There is no better biological example of an intelligent inference.

Around the Blogosphere 1/4/07

'Intrinsic Control and Junk DNA'
by MikeGene

"Several years ago, I commented on how James Shapiro’s views of evolution are actually quite friendly to ID. Appreciation of this point requires the recognition of a subtle point." Find what follows at:

At Uncommon Descent:

'Molecular Clocks: Michael Denton continues to be vindicated' by scordova

'PoL #2: Very Special'
by MikeGene

"In my previous blog, I hint that Marc Kirschner and John Gerhart are on the right track in focusing on deep conservation. Just what might it mean? Well, among other things, consider this:"

See what follows at:

At Uncommon Descent:

Sea Urchin Design by DaveScot

Such power, such grace by Kevin Miller

Tuesday, January 02, 2007

Science vs. Scientism

Chuck Colson's essay Brooking No Debate underscores the intolerance of an aggressive strain of atheism in evidence at a conference that, in Colson's words, "turned into the secular materialist equivalent of a revival meeting." At the conference Steven Weinberg, a physicist, was quoted as saying “the world needs to wake up from its long nightmare of religious belief.” Quoting from the essay:

"Another, physicist Lawrence Krauss, chided them, saying “science does not make it impossible to believe in God . . . [and] we should recognize that fact . . . and stop being so pompous about it.”

Fat chance. What’s behind all of this animosity? It is a worldview known as “scientism,” the belief that there is no supernatural, only a material world. And it will not countenance any rivals. It is a “jealous god.”

As Weinberg’s comments illustrate, it regards any other belief system other than scientism as irrational and the enemy of progress. Given the chance, as in the former Soviet Union, it wants to eliminate its rivals. It is no respecter of pluralism."

No it is not but it is worth recalling the words of perhaps the greatest of all physicists:

"The scientist's religious feeling takes the form of
rapturous amazement at the harmony of natural law, which reveals an intelligence of such superiority that, compared with it, all the systematic thinking and acting of human beings is an utterly insignificant reflection."
Einstein (The World As I See It, p.9)

and this too from Einstein:

"Then there are the fanatical atheists whose intolerance is the same as that of the religious fanatics, and it springs from the same source… They are creatures who can't hear the music of the spheres."

Back to Colson:

"The naturalists, on the other hand, rule out even science that tends to show intelligence, because that might lead to a God. Now, who is narrow-minded?"

Narrow-minded and with a desire to control others; a most unpleasant combination.