Intelligently Sequenced

Human Biological Diversity

2011-04-04T21:45:00.000-07:00

Here is a new HBD Bibliography: http://www.humanbiologicaldiversity.com/

It's a collaborative effort, so send corrections and suggestions (even of your own work) to: hbdbibliography@gmail.com

12 Creationist blogs

2011-03-11T07:35:00.000-08:00

I got this message from Tim Dalton:

We just posted an article, “Understanding Creationism: The Top 12 Creationist Blogs”. I thought I'd bring it to your attention in case you think your readers would find it interesting.

For myself, I would add Creation-Evolution Headlines.

James Madison

2011-01-11T18:19:00.000-08:00

The Origin of Gene Expression

2010-11-27T16:07:00.000-08:00

Crystal structure of a reverse polymerase is a paper published by PNAS. Its authors are John J. Perona and Javin P. Oza. The first sentence reads: "The primary transcripts of transfer RNA (tRNA) molecules undergo extensive processing and chemical modification to become functional components of the protein synthesis apparatus." Transfer RNA (tRNA) plays a central role in some origin of life scenarios describing how a genetic code might have arisen in a precellular environment. Cells must translate information stored in DNA to enable protein synthesis. Codons correlating to specific amino acids need to be paired and properly sequenced so as to make possible functional sequences of polypeptides. Sets of enzymes known as tRNA synthetases ensure the attachment of a specific amino acid to a specified tRNA.

The paper alludes to modification of primary tRNA transcripts. Chemical modification makes functional specificity possible. Described is an instance of guanosine attachment to tRNA making recognition by histidyl-tRNA synthetase possible. Plausible scenarios for the evolution of gene expression modification components are possible but some degree of minimal cellular functionality is a prerequisite in the view of this writer.

That view is sometimes criticized as an argument based on personal incredulity. That's an odd critique in view of the fact that specified pathways are in acutely short supply. What's the opposite of personal incredulity? Unquestioning faith? Sounds close. If skepticism is grounded in the complexity of that which is observed and a process allowing that x, y and z can evolve depends on greatly complex cellular components being in place, then an absence of the foregoing should elicit skepticism in the mind of all but unquestioning believers.

It's Not Easy Being Green but it is Very Lucrative

2010-10-02T08:10:00.000-07:00

Salvador Cordova wrote Sanford’s pro-ID thesis supported by PNAS paper, read it and weep, literally. Quoting:

Cornell Geneticist John Sanford argued that Darwinism is wrong because the rate of genetic deterioration is so high that natural selection could not arrest it. If natural selection cannot arrest genetic deterioration, how then could it be the mechanism for evolutionary improvement?

Sanford predicted through his research that human genome is deteriorating. This was a daring scientific prediction, and now Michael Lynch of the elite National Academy published on the topic for his inaugural paper. The NAS has now made the paper available to the public free of charge.

Read it, and weep, literally:

Rate, Molecular Spectrum, and Consequences of Human Mutation

A focus on the human mutation rate is not new. It has been noted by James Crow- The high spontaneous mutation rate: Is it a health risk? and by Nachman and Crowell- Estimate of the Mutation Rate per Nucleotide in Humans. Nachman and Crowell take note of a paradox made apparent by the "high deleterious mutation rate in humans." They concluded by remarking that "the results presented here indicate that some form of positive epistasis among deleterious mutations is likely."

This quote appears at Telic Thoughts:

the impact of deleterious mutations is accumulating on a time scale that is approximately the same as that for scenarios associated with global warming

LOL.

Being ever alert in noting newly evolved species of social causes, that caught my attention. I think we could be witnessing a new cause in the making. This, like some many of its ancestors, holds forth great promise. The threat- high human mutation rates. The effect- disease and death. The genesis of a new social movement is apparent. After all the global warming movement was built around much less. From Crow's paper:

My concern, however, is not with mutation as a cause of evolution, but rather as a factor in current and future human welfare. Since most mutations, if they have any effect at all, are harmful, the overall impact of the mutation process must be deleterious. And it is this deleterious effect that I want to discuss.

Great stuff. All the elements are present. Concern. Human welfare. Motivating one to want to discuss deleterious effects. Can legislation be far behind? And oh that funding. Hope the tea baggers don't sabotage the fun. But there is more:

I conclude that for a number of diseases the mutation rate increases with age and at a rate much faster than linear. This suggests that the greatest mutational health hazard in the human population at present is fertile old males. If males reproduced shortly after puberty (or the equivalent result were attained by early collection of sperm and cold storage for later use) the mutation rate could be greatly reduced.

You can sense where this is heading. Go for it man. But alas there was this disappointing remark:

I am not advocating this.

C'mon, take a stand. Don't wimp out on us before the cause even gets untracked. We don't have the rules and (more importantly) the money arranged yet. Sometimes you just have to look at the pros to see how to ruin (or advance) a cause. From Greens Shackle National Security - and Renewable Energy:

A more likely reason is that the Chinese want to manufacture the finished goods, thereby creating countless “green” factory jobs, paid for with US and EU taxpayer subsidies, channeled through GE, Siemens, Vestas and other “socially responsible” companies that then install the systems across Europe and the USA.

The Chinese economy is not growing for lack of good planning and is seizing on opportunities that leftist zealots in the West present. Kermit said something about how good it is to feel green. The Chinese know of the wisdom of that frog. Let the west feel good while they take their money. All for the environment of course. The white west is soooo smart. No wonder arrogance is the norm on MSNBC while outrage pervades the electorate. And there is this too:

The Indian government is planning to launch a $11 billion fund to help finance the massive power generation planned during 2012-2017.

and this nugget:

Coal remains the backbone of the generation sector in India with more than 55 percent of the power generated by coal-fired power plants

Lest we forget China’s Thirst for Oil.

China’s growth has been stellar with high GDP numbers reported yearly. In 2009, Chinese crude oil imports accounted for 52% of the country’s total oil consumption, up from 45% in 2006. Importing more than 50% is recognized as an energy security alert. By 2020, analysts believe that 65% of the oil consumed in China will have to be imported. Not that long ago, China was an oil exporter in 1992.

Yes folks, those solar panels and wind mills made in China come out of some very fossil fuel run factories. So what are we looking at here? Vast increases in the amount of fossil fuels consumed in China, India and other developing economies in Asia and Africa. This outputs (and will output even more in the near future) vast amounts of CO2, dwarfing any savings in the prissy west. If you developed warm feelings for the green cause while attending an institution of higher learning and get the feeling you have been had you are right on. The white man's burden is heavy but it is not being shouldered by some very savvy businessmen in Europe and America who stay ahead of the regulatory curve. Rather the burden for our environmental fantasies fall on working class stiffs on both continents.

If we could get our green marketing directors headed over to Crow's lab they just might develop the seed of a good social cause and funnel some more cash to research into disease in the process. It would do more good than the current social justice mania.

Loss of Rights or Toleration for the Intolerant.

2010-09-22T10:29:00.000-07:00

Which way should we allow it to backfire?

Taking away some rights of others to do whatever they’d like to do – the backfire being that this might (further down stream) provide precedent for reasons as to why some of our rights should be taken away.

-or-

Being tolerant of a worldview that is intolerant to our way of life (culture, religious identity) – the backfire being that their worldview (when their numbers increase enough) forced upon us causes us to lose our way of life; our ability to freely practice the things that gave our culture its identity.

In the former, we’re still the ones from which our governmental leaders come from. They are here to serve the mass of people; we are not here to serve them. So, the principle would still exist that the majority, who give the government the power it has, can take power away from its leaders.

In the latter, we’re second class citizens (dhimmi). We no longer have that principle to enforce. Vocalization of the principle falls on deaf, unconcerned ears. We sacrificed one right following the former – we lost them all following the latter.

History more consistently supports the likeliness of one scenario over the other. Tolerance for the intolerant per se never played in our favor. I just hope there’s another Charles Martel or Jan Sobieski amongst our ranks….. it looks like we’ll be needing them.

Wiki and DNA Repair

2010-09-18T04:10:00.000-07:00

There are many posts at Intelligently Sequenced within the label "DNA Repair." Wikipedia has an article on this topic. This is from it:

In contrast to DNA damage, a mutation is a change in the base sequence of the DNA. A mutation cannot be recognized by enzymes once the base change is present in both DNA strands, and thus a mutation cannot be repaired. At the cellular level, mutations can cause alterations in protein function and regulation. Mutations are replicated when the cell replicates. In a population of cells, mutant cells will increase or decrease in frequency according to the effects of the mutation on the ability of the cell to survive and reproduce. Although distinctly different from each other, DNA damages and mutations are related because DNA damages often cause errors of DNA synthesis during replication or repair and these errors are a major source of mutation.

Given these properties of DNA damage and mutation, it can be seen that DNA damages are a special problem in non-dividing or slowly dividing cells, where unrepaired damages will tend to accumulate over time. On the other hand, in rapidly dividing cells, unrepaired DNA damages that do not kill the cell by blocking replication will tend to cause replication errors and thus mutation. The great majority of mutations that are not neutral in their effect are deleterious to a cell’s survival. Thus, in a population of cells comprising a tissue with replicating cells, mutant cells will tend to be lost. However infrequent mutations that provide a survival advantage will tend to clonally expand at the expense of neighboring cells in the tissue. This advantage to the cell is disadvantageous to the whole organism, because such mutant cells can give rise to cancer. Thus DNA damages in frequently dividing cells, because they give rise to mutations, are a prominent cause of cancer. In contrast, DNA damages in infrequently dividing cells are likely a prominent cause of aging.

Bethell about Eric Hoffer

2010-08-31T19:24:00.000-07:00

Eric Hoffer's Skepticism About Darwinism appears at Evolution News and Views. From the article:

He had written that "when God died in the middle of the 19th century there was immediately set in motion a process which tended to reverse the separation of nature and human nature." Darwinism, and the intellectual currents of his day, "aimed to reduce human nature to nature." Biologically, man was now seen as nothing more than "a superior monkey." Politically, he was an automaton who could be manipulated by a Mao or a Stalin.

Hoffer's refusal to join the parade of thinkers who accepted that man was little more than a boastful ape was perhaps his finest hour as a philosopher. It showed him at his most independent. And his perception of the unique qualities of man encouraged him to ponder man's Creator.

DNA DSBs and Genomic Integrity

2010-07-31T05:19:00.000-07:00

Androgen-induced TOP2B-mediated double-strand breaks and prostate cancer gene rearrangements, Michael C. Haffner et. al. (Nature Genetics 42, 668–675 (2010)), reminds us that DNA double-strand breaks can induce genomic rearrangements and cancer. The study relates DSBs to androgen signaling.

Organisms have remedial tools able to check potentially devastating effects of DSBs. How viable are multi-cellular life forms without such tools? The answer indicates a natural entry for a front loading concept.

Network Topologies and Biochemical Adaptation

2010-06-29T14:08:00.000-07:00

Key Circuits Control Cell's Ability To Adapt To Changes In Its Environment is a Science Daily article. Quoting from it:

ScienceDaily (2009-08-25) -- Researchers have identified the two key circuits that control a cell's ability to adapt to changes in its environment, a finding that could have applications ranging from diabetes and autoimmune research to targeted drug development for complex diseases.

A paper on the finding was published in the August 21, 2009 edition of the journal Cell. The article is titled
Defining Network Topologies that Can Achieve Biochemical Adaptation. Biochemical adaptation is an issue around which controversy has centered during discussions of intelligent design. Michael Behe comes readily to mind.

The Science Daily article places some emphasis on adaptation to stimulus, cellular reset and homeostasis. Researchers analyzed millions of cellular circuits involved in adaptive responses. The complexity of the analysis is impressive. Interestingly a study of enzymatic regulatory networks resulted in the identification of "two core structures that are common to every adaptive response."

Clean up Environmental Disasters- but only if your Politics is Correct

2010-05-23T03:47:00.000-07:00

The Washington Times posted an alarming article alluding to practical abuses of unbridled political correctness. I should qualify the term alarming because censoring or punishing a scientist because his views are unacceptable to the far left is comforting to the closet fascists among us.

The article indicates that the Energy Department removed a St. Louis scientist from a consulting position. The responsibilities of that position included the pursuit of solutions to the Gulf of Mexico oil spill. The disturbing part is that the removal was said to be linked to the views of this scientist on homosexuality and race relations.

Leftist scientists are noted for leaving their brains in the lab when social issues come to light so let's spell this out. Physics professor Jonathan Katz was selected for the position because there is an environmental crisis (obvious I know but you need to drill the obvious into ideologues) and Katz's expertise was valued. In other words he could help alleviate the consequences of the disaster. We know how much leftists hate environmental harm right? Global warming, global warming, global warming...

On the other hand we simply cannot have homophobes running wild in America. And the race card? Bring out the whole deck fellows. We all know that free speech is to be tolerated only when gay rights and racial profiling agendas are treated with due homage. Bend your knee toward PC norms or be fired. I hope Katz has tenure because he's up against a powerful political clique.

A gay rights advocate was quoted as saying:

It's disappointing at a time like this that when all Americans need to come together and focus on relief efforts and recovery efforts in the Gulf, someone divisive was placed in a position of power

He admits the need to solve a crisis and to have us come together to do so. He and his fellow ideologues then throw a helpful scientist overboard because of his politics and blame "divisiveness". Divisiveness is a code word for an opposing point of view.

When Ben Stein alleged that intolerance was rampant in academia (and by logical extension academics who run the government) maybe he was on to something after all.

When Meaning Transcends How it Works

2010-04-02T18:49:00.000-07:00

The following was also published at Telic Thoughts.

Regis Nicoll wrote The Bad News of Intelligent Design which appears at the Break Point website. I submitted a comment which a commenter named Steven J. Thompson responded to. His remarks provide the context for my own arguments. Thompson's remarks are contained within the blockquotes:

Regis Nicoll offered an argument from consequences: ID, he claims, offers a support for moral choices he approves and undercuts support for moral choices he disapproves.

I would agree with Nicoll but would add that intelligent design disciplines like archeology and history offer more powerful support for the faith and morality he embraces. Undercutting views opposed to Christian moral norms is considered threatening to some ID critics. Why else would they moan about a Trojan horse? They are alarmed that ID could herald the propagation of Judeo-Christian values they abhor.

I was arguing, simply, that he was wrong: if we don't know and aren't allowed assumptions about the Designer's methods, motives, and design philosophy, then we have no grounds whatsoever for inferences about how much or under what circumstances the Designer values His creations, or how He expects us to behave (including either "all human life is sacred" or "some human life is not sacred").

Thompson is right to argue that intelligent design cannot answer important questions about our Creator and his expectations of us. That information must be revealed to us by God.

Intelligent Designers keep insisting, whenever they are arguing that their ideas are science rather than religious apologetics, that the Designer doesn't need to be the Christian God, or God at all. I'm simply pointing out the implications of that position.

IDists argue that a design inference tells us nothing about the character of a designer.

Intelligent design purports to be a scientific argument. The imputation of design is supposed to be a scientific hypothesis, if not an outright scientific conclusion. What possible sense does it make to say that it does not need to be empirical?

Intelligent design is influenced by realities of the physical world. ID might be considered protoscience. It surely has philosophical aspects but they are constrained by the natural world. Conservation of information concepts may lead to a full fledged scientific discipline or only to interesting musings. But ID is not delinked from empirical data even if it does not provide the theoretical framework needed for a research program.

There can be arguments for theism that are not empirical, but they cannot be design arguments (and conversely, again, a design argument is not necessarily an argument for an omnipotent, omniscient, omnibenevolent God with a plan for our salvation).

Non-empirical arguments for theism cannot be design arguments? Why not? That seems irrational to me. But I would agree that a design argument is not an argument for a God with a plan for our salvation.

I don't think you quite grasp the "God of the gaps" accusation. Edward O. Wilson argued, on strictly naturalistic and evolutionary grounds, that there were probably natural phenomena that humans would never be able to explain. Conceivably, the origin of life could be such a permanently intractable problem. I think it was Isaac Asimov who stated that he was convinced that unidentified flying objects existed; it was their identification as alien space ships that he questioned. By the same token "we don't know how this happened" is not evidence for intelligent causation, much less for any particular sort of intelligent Cause.

This is a straw man. IDists do not make this argument.

ID doesn't have even a hint of a mechanism by which "intelligence" creates life (in our experience, so far as it goes, all the intelligence in the world won't put a line on paper, much less build a complete machine from a blueprint, without some sort of material mechanism), so what scientific advantage does it enjoy over "some unknown natural cause presumably did it?"

Several things need to be noted. That the presumption of a material mechanism is not evidence for it or even an indicator that a theoretical mechanism exists, is not even the problem alluded to by intelligent design. Even when you have an identifiable mechanism you still have not identified a causal source for a distinctive outcome accomplished through the endeavors of intelligent agency. Messaging is a case in point. Fingers and muscles are part of the mechanistic complex explaining the physical forces creating this message. But since the mechanism is directed by a mind, which could create a completely contrary message or none at all, the identification of a mechanism is of trivial significance to a determination of the message itself.

Yet a message can convey evidence of a conscious intelligent source. Consider the messaging inherent to gene expression. Biochemical processes give evidence of physical mechanisms involved in initiating, curtailing and realizing cellular changes. All made possible by a convention described as a genetic code. Sequencing of identical nucleotides can signal different amino acids, different proteins and ultimately alternative functions. Alternative sequencing within an established convention is a mark of symbolism which in turn indicates an abstraction i.e. meaning made intelligible by a mind.

Materialists argue that the symbolism alluded to is seeming i.e. the product of blind forces of nature simulating an abstraction. It may appear to be the case that UCC is the physical representation of serine and it indeed is but one may draw no conclusion that the linkage resulted from anything other than a combination of stereochemical forces, random environmental conditions and some unspecified natural selection dynamic. All as impersonal and intelligence free as the force drawing a batted ball toward the ground. This has not shown to be the case of course but the operative assumption is that this lack of empirical confirmation is attributable to a lack of knowledge which will yield to a breakthrough in the future. To doubt this is to engage in placing God into the gaps of our knowledge; as if God was removed from the realm of possibility by virtue of our discovery of how his creations function.

In a previous post John Polkinghorne was quoted as saying:

Science tells us how the world works, but it really doesn’t try to tell us about matters of meaning or value or purpose, which are equally important.

Messages have meaning, value and purpose consistent with a conscious intelligent origin source. UCC/serine is not a poetic or fanciful abstraction imposed by an observant mind yet unconnected to physical reality as is the imagery that a cloud pattern might evoke in a creative mind. Constraint is a distinguishing factor. The interpretation a mind applies to distinguish design from non-design is not dictated or precluded by empiricism. Rather it results from meaning assigned to physical symbols by a conscious intelligent mind. We don't know how God could happen is not an argument for the origin of a blind watchmaker. Don't use materialism to bridge the cognitive limitations of humans.

Science has boundaries demarcated by the accuracy and extent of its predictions. Meaning is not defined by scientific limitations. Rational linkages constrained by nature provide meaning. That meaning points to intelligent design as a likely causal source. Consistent with philosophical materialism? No. The result of identifying a physical mechanism? No. As rational as the materialist driven attribution of an unidentified mechanism? No. It's more rational in that the known logic, knowledge and workings of conscious intelligence favorably contrast with the fuzzy ill-defined machinations of physical theories for a causal explanation of functionally sequenced DNA.

Another Side to the Natoma Canfield Story

2010-03-17T07:06:00.000-07:00

The poster child for the Obama/Pelosi/Reid express pushing the government take over of our health care system is Natoma Canfield. Canfield is a cancer patient shamelessly used by power brokers to effect their own ends. Aw the emotion. Don't you feel bad for her. Yes. She is going to die like the rest of us and the question becomes when and how long can the inevitable be postponed. Not very touchy feely but true.

The factual questions in this political drama centered around Natoma Canfield are how much are her treatments costing, who should pay for them, what is her long term prognosis with or without treatment, will she lose her home and will she get assistance in paying her bills. But don't look to the Obama/Pelosi/Reid cabal for answers. They have their own agenda and the truth is often a casualty of it.

Clinic: Cancer Patient Who Wrote to Obama Will Not Lose Home, May Get Aid, is an article containing statements not heard from the President while he was campaigning for socialized medicine in Ohio. Quoting:

Natoma Canfield, the cancer-stricken woman who has become a centerpiece of President Obama's push for health care reform, will not lose her home over her medical bills and will probably qualify for financial aid, a top official at the Cleveland medical center treating her told FoxNews.com.

Oh but that was a Fox news source and you know what those kind of people are like Bradford or at least you would if you were a good progressive. Fine, let's go to a drive by media source:

And the Cleveland Clinic said it has no intention of putting out a lien on Canfield's house — or letting the billing process interfere with her treatment.

"It appears that I think she'll be fine," said Lyman Sornberger, the hospital's executive director of patient financial services. "By nature of the fact that she was not early on rejected by either program, that's a key indicator that she will most likely be eligible."

at: Clinic: Woman Championed by Obama Eligible for Aid

The truth matters. Some might be inclined to think it might matter even for politicians. I'd argue it does matter especially for politicians.

The Mythology of Secular Common Ground

2010-03-04T15:13:00.000-08:00

I wrote the following blog entry which was posted at Telic Thoughts. The piece provoked a number of amusing comments. Their authors supported the assumptions of Stanley Fish albeit unintentionally.

Stanley Fish wrote a brilliant opinion piece in the New York Times titled Are There Secular Reasons? Tom Gilson authored a blog entry on it at Thinking Christian. Fish takes notice of a debate centered around the role of religion in public life and cites an argument from Classical Liberalism that policy decisions should be formulated based on secular reasons and not values which are linked to a religious source. Fish goes on to describe this as a form of "intellectual/political apartheid known as the private/public distinction." He develops these thoughts is some detail and then refers to a new book by law professor Steven Smith titled The Disenchantment of Secular Discourse. The first paragraph at the link is a good one:

Prominent observers complain that public discourse in America is shallow and unedifying. This debased condition is often attributed to, among other things, the resurgence of religion in public life. Steven Smith argues that this diagnosis has the matter backwards: it is not primarily religion but rather the strictures of secular rationalism that have drained our modern discourse of force and authenticity.

Discussions which rule out entire blocks of thinking a priori are destined to be dull and unedifying. Moreover they cannot be searches for truth as they substitute dogma in a divide which thirsts for delineation of genuine alternatives. Fish writes this:

It is not, Smith tells us, that secular reason can’t do the job (of identifying ultimate meanings and values) we need religion to do; it’s worse; secular reason can’t do its own self-assigned job — of describing the world in ways that allow us to move forward in our projects — without importing, but not acknowledging, the very perspectives it pushes away in disdain.

Fish nails it. Identifying "secular values" entails smuggling intrinsically religious meanings and values into a secular nexus. Moreover attempts to "keep it secular" must deny this core element of secularism affording it an edifice based on a dishonest premise. Consider some of the major discussion points in America today. Global warming well illustrates the point. My own experience confirms the wisdom of Smith for when arguments proceed against global warming policies predictable responses point to data supporting global warming. Not one to hide my reasons I remind others that there is a good deal more to the issue than whether or not a warming trend exists. Opponents of global warming policies need to bear this in mind as well. When vast sums of money are earmarked for legislation in support of a cause's goals, underlying moral issues are always linked to it. To avoid rehashing the many arguments we can simply cut to the chase and point to alternative uses such funding could be put to in illustrating the balanced scale metaphorical description of any final choice. The persistent stuck in neutral arguments about warming indicate that at least some are caught up in the thinking that the tough moral decisions are dictated by temperature graphs. Yup, it's warming or no it is not is the starting point and not the conclusive dictum required. There are similar problems in the debate about health care and in the "origin of morality"- a fine piece of junk science if there ever was one. A book is needed on this. Fish says this more eloquently:

No matter how much information you pile up and how sophisticated are the analytical operations you perform, you will never get one millimeter closer to the moment when you can move from the piled-up information to some lesson or imperative it points to; for it doesn’t point anywhere; it just sits there, inert and empty.

HT: Nullasalus

News Links: the Climate Change Movement

2010-02-15T20:35:00.000-08:00

Here are some links to stories related to the ongoing controversies related to the climate change movement:

World may not be warming, say scientists

Surface temperature records: policy driven deception? - a report by Joseph D’Aleo and Anthony Watts

Climategate U-turn as scientist at centre of row admits: There has been no global warming since 1995

How Climate-Change Fanatics Corrupted Science

HT: Clare

A Grasshopper and an Ant

2010-01-31T18:20:00.000-08:00

THE ANT AND THE GRASSHOPPER:

This one is a little different... Two Different Versions... Two Different Morals

OLD VERSION

The ant works hard in the withering heat all summer long, building his house and laying up supplies for the winter.

The grasshopper thinks the ant is a fool and laughs and dances and plays the summer away...

Come winter, the ant is warm and well fed.

The grasshopper has no food or shelter, so he dies out in the cold.

MORAL OF THE STORY: Be responsible for yourself!

MODERN VERSION

The ant works hard in the withering heat and the rain all summer long, building his house and laying up supplies for the winter.

The grasshopper thinks the ant is a fool and laughs and dances and plays the summer away.

Come winter, the shivering grasshopper calls a press conference and demands to know why the ant should be allowed to be warm and well fed while he is cold and starving.

CBS, NBC , PBS, CNN, and ABC show up to provide pictures of the shivering grasshopper next to a video of the ant in his comfortable home with a table filled with food.

America is stunned by the sharp contrast.

How can this be, that in a country of such wealth, this poor grasshopper is allowed to suffer so?

Kermit the Frog appears on Oprah with the grasshopper and everybody cries when they sing, 'It's Not Easy Being Green.'

ACORN stages a demonstration in front of the ant's house where the news stations film the group singing, "We shall overcome " . Then Rev. Jeremiah Wright has the group kneel down to pray to God for the grasshopper's sake.

President Obama condemns the ant and blames President Bush, President Reagan, Christopher Columbus, and the Pope for the grasshopper's plight.

Nancy Pelosi & Harry Reid exclaim in an interview with Larry King that the ant has gotten rich off the back of the grasshopper, and both call for an immediate tax hike on the ant to make him pay his fair share..

Finally, the EEOC drafts the Economic Equity & Anti-Grasshopper Act retroactive to the beginning of the summer.

The ant is fined for failing to hire a proportionate number of green bugs and, having nothing left to pay his retroactive taxes, his home is confiscated by the Government Green Czar and given to the grasshopper.

The story ends as we see the grasshopper and his free-loading friends finishing up the last bits of the ant's food while the government house he is in, which, as you recall, just happens to be the ant's old house, crumbles around them because the grasshopper doesn't maintain it.

The ant has disappeared in the snow, never to be seen again.

The grasshopper is found dead in a drug related incident, and the house, now abandoned, is taken over by a gang of spiders who terrorize the ramshackle, once prosperous and once peaceful, neighborhood.

The entire Nation collapses bringing the rest of the free world with it.

MORAL OF THE STORY: Be careful how you vote in 2010.

Thanks for that Clare.

Impact of Segregation of Chromosomes During Mitosis on Genomic Integrity

2010-01-23T17:18:00.000-08:00

Mechanisms of chromosome behaviour during mitosis is a paper authored by Claire E. Walczak, Shang Cai and Alexey Khodjakov which appears in the journal Nature Reviews Molecular Cell Biology. It discusses chromosomes and mitosis as well as genomic fidelity. We would expect to find multiple mechanisms preserving genomic integrity in intelligently sequenced genomes. We are not disappointed.

The behavior, which is the focus of the cited paper, has to do with interactions between chromosomes and spindle microtubules. The interactions are described as highly regulated. The paper contains the following remark:

Recent discoveries, enabled by high-resolution imaging combined with the various genetic, molecular, cell biological and chemical tools, support the idea that establishing and controlling the dynamic interaction between chromosomes and microtubules is a major factor in genomic fidelity.

A Cellular Response to Broken Chromosomes

2009-12-28T18:20:00.000-08:00

Science Daily features an article titled How Cells Handle Broken Chromosomes. Quoting from the article:

Scientists have discovered a novel cellular response towards persistent DNA damage: After being recognized and initially processed by the cellular machinery, the broken chromosome is extensively scanned for homology and the break itself is later tethered to the nuclear envelope. The researchers have uncovered a surprising feature of how DNA strand breaks can be handled.

The writer notes elaborate DNA repair systems involved in the repair of DNA double strand breaks (DSB). Researchers observed a "tethering" of yeast DSB to the nuclear envelope. It was speculated that this might prevent errors engendered by recombination. Rad51, sometimes dubbed recombinase, spreads over the chromosome containing the break during the repair process. Another protein, H2A.Z, is also essential for the activation of Rad51 and relocating DSBs to the nuclear envelope. When H2A.Z is not present in cells such cells are very sensitive to DSBs.

Valid Epistemology

2009-11-20T04:51:00.000-08:00

JAD, at Telic Thoughts, recently made a comment containing these remarks:

In the same way, the empirical study of a natural process is, is a cumulative process that is never sufficient, to give us absolute knowledge. It is, furthermore, illegitimate to claim that a philosophical worldview, supposedly based on scientific evidence, is any more certain or reliable than an alternative world view the interprets the evidence differently. And, it is arrogant to argue that the alternative is irrational.

1500+ years ago St. Augustine observed:

“Miracles do not happen in contradiction to nature, but only in contradiction to that which is known to us of nature.”

It appears that, Mr. Augustine, also understood the limitations of inductive reasoning.

A fundamental reason why knowledge, acquired solely as a consequence of empirical efforts, cannot be deemed superior to alternatives lies with the limitations of empirical investigations. Science is limited and so too is the authority of philosophical positions based on scientific data.

Augustine also was correct in noting that it is our knowledge of nature which sets parameters for what is miraculous. Sometimes though one can be confident in that knowledge. Rising from the dead after several days would be a reliable indicator.

Teleology

2009-10-18T09:37:00.000-07:00

Allen MacNeill and Rock are two of the more thoughtful commenters at Telic Thoughts. Allen recently wrote a comment containing these remarks:

The presence or absence of design or purpose (technically teleology) in nature is not a "finding", it is an inference. That is, the presence or absence of teleology cannot be directly observed, nor can it be indirectly observed (as is the case for, say, atoms).

Rather, the presence or absence of teleology can only be indirectly inferred on the basis of its necessity. If teleology (i.e. pre-existing or "foresighted" design) were necessary to bring about those objects and processes we observe in nature, then it would be necessary to infer their existence and operation. Hence Dr. Behe's arguments for "irredicible complexity" and Dr. Dembski's arguments for "complex specified information", both of which they assert are arguments for the necessary intervention of a supervening "designing force" in evolution. In brief, if "you can't get here from there" without teleology, then teleology becomes an inference that flows from your analysis.

This means that the inference to teleology is an inference by exclusion. Only when one has conclusively shown that the observable objects and processes in nature cannot have come about via non-teleological processes is it legitimate to infer teleology. To be as clear as possible: teleology is a post hoc inference, not a propter hoc assumption. This is why scientists (at least those who practice in the "natural" sciences, such as biology, chemistry, and physics) do not assume the existence of teleology. Rather, we attempt to explain those objects and processes we observe without resorting to post hoc inferences, such as teleology.

That comment induced this response by JAD containing these remarks:

It’s true that teleology is a metaphysical inference, but so is dysteleology (to use the term the Ernst Haekel coined.) And, I think that both sides should be free look at the evidence and argue for their respective interpretation and/or point of view. However, such interpretations are not strictly empirical interpretations, rather they are top-down interpretations that are based on presumptions and assumptions that are themselves unproven and perhaps are un-provable. If we limit natural science to things that can be studied empirically, then both teleology and dys-teleology fall outside those limits.

I do think that there are some minimal metaphysical assumptions that are necessary to do natural science. For example, I think that we need to assume that there really is real world out there, and that the laws of nature are for all intents and purposes universal, acting the same everywhere throughout the whole history of the universe. These are a couple but not all the assumptions, that we need to do science, at least if we extrapolate our study into the past or into the future.

However, I don’t see why it is necessary for a scientist to assume that the universe, or the natural processes we observe in the universe have no plan no purpose or no ultimate meaning. If that is your philosophical or theological interpretation, fine. Argue for it in that way. But, it is not, in itself, an empirical argument, and neither is it a position one needs to accept metaphysically or methodologically to do science.

In other words, dysteleology is a post hoc inference, not a propter hoc assumption. And, it is unnecessary to do science.

History is full of examples of scientists who metaphysically saw God in nature and yet have made major discoveries and contributions. My favorite is, Johannes Kepler, who said about his scientific work:

"I was merely thinking God's thoughts after him. Since we astronomers are priests of the highest God in regard to the book of nature, it benefits us to be thoughtful, not of the glory of our minds, but rather, above all else, of the glory of God."

...as well as a comment of my own:

If you can't get there except through teleology then a teleological inference is imperative but you might be too exclusionary in your your application of a necessity standard. Direction is sufficient and bias toward outcomes of stochastic processes, which are inconsistent with probability assessments, can infer teleology. The difference can be subtle but important. A strict necessity paradigm requires a concurrent standard of demonstrating impossibility. Not only is that requirement too stringent, it may be impossible. But if observed outcomes deviate from expectations (but fall within physical possibilities) then biased outcomes are evident. If a biased stochastic process is not attributable to physical causality then a prima facia case is made for teleology.

The downside to this is a teleological predisposition toward expectations of non-teleology. We see this with some "gap" issues like the origin of life. If you cannot empirically derive non-teleological explanations based on finding suitable causes for mappings of codons to amino acids you maintain that necessity is implicated but not yet pinpointed. This is the flip side to exclusionary requirements. If some demand the demonstration of impossibility for teleology they likewise apply an always possible standard to expectations of non-teleology. That representation of a specific amino acid could not have been the causal result of conscious assignment even indirectly. It must have incidentally resulted from unexplained physical necessity coupled to a stochastic process. Conscious symbolism is unintentionally mimicked by a blind code maker.

JAD was spot on when he pointed out that "dysteleology is a post hoc inference, not a propter hoc assumption. And, it is unnecessary to do science." The meaning of concepts is framed by contrasting concepts. Old earth creationists are contrasted to young earth creationists. The contrast highlights the uniqueness of respective points of view. Dysteleology, as the default position for science, requires a rationale justifying its preferred status or it ceases to offer a meaningful contrast to teleology. Teleology is intrinsic to life. Survival and reproduction are obvious goals. Why are causal trails associated with them considered dysteleological when complete causal trails remain unelucidated?

Schindewolf on Paleontology

2009-10-14T07:00:00.000-07:00

TT commenter Daniel Smith posted a comment at Telic Thoughts containing the following remark:

Most evolutionists won't read Schindewolf because his anti-Darwinian hypothesis is so fully developed. "Basic Questions in Paleontology" is a dangerous book for the 'Darwinist' (by that I mean all those attached to modern synthesis). Schindewolf cites mountains of evidence based on decades of painstaking research. His case is devastating to the 'undirected evolutionary' mindset – so they avoid it like the plague. The nearest they will get is to read Stephen Jay Gould's foreword and consider Schindewolf's ideas refuted because Gould discounts them. I guess the argument from authority is always good enough so long as it backs up your worldview.

I have not read Schindewolf but the comment has piqued my interest. For the Wikipedia entry on Otto Schindewolf click here.

How Nature Stores Information

2009-10-14T02:45:00.000-07:00

idnet.com.au posted A stunningly elegant solution to storing information at Uncommon Descent. It links to Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome by Erez Lieberman-Aiden et. al. At issue among other things are specifics related to storing genetic information and the compartmentalization of DNA within the nucleus. Different locations hold active and inactive genes. There is a dynamic flow correlating to gene expression. DNA has the capacity to condense and form a very dense structure able to fold and unfold to suit cellular needs.

On Intrinsic Intentionality

2009-09-26T06:09:00.000-07:00

Techne returned to Telic Thoughts to post this entry. I enjoy his posts and comments. There was a link in the OP to Nano-Intentionality - A Defense of Intrinsic Intentionality which is authored by W Tecumseh Fitch. Quoting the abstract:

I suggest that most discussions of intentional systems have overlooked an important aspect of living organisms: the intrinsic goal-directedness inherent in the behaviour of living eukaryotic cells. This goal directedness is nicely displayed by a normal cell's ability to rearrange its own local material structure in response to damage, nutrient distribution or other aspects of its individual experience. While at a vastly simpler level than intentionality at the human cognitive level, I propose that this basic capacity of living things provides a necessary building block for cognition and high-order intentionality, because the neurons that make up vertebrate brains, like most cells in our body, embody such capacities. I provisionally dub the capacities in question "nano-intentionality": a microscopic form of "aboutness". The form of intrinsic intentionality I propose is thoroughly materialistic, fully compatible with known biological facts, and derived non-mysteriously through evolution. Crucially, these capacities are not shared by any existing computers or computer components, and thus provide a clear, empirically-based distinction between brains and currently existing artificial information processing systems. I suggest that an appreciation of this aspect of living matter provides a potential route out of what may otherwise appear to be a hopeless philosophical quagmire confronting information-processing models of the mind.

Events Leading to the Great Bailout: Part Two

2009-09-14T09:15:00.000-07:00

In a previous post Thomas Sowell's book The Housing Boom and Bust was used as a source reference to explain some fundamental problems that led to a subsequent economic disaster and the historic bailout. The problems cited involved supply and demand and legal restrictions on land use that decreased land availability for home construction.

This blog entry will draw from information supplied in the second chapter of The Housing Boom and Bust. Sowell notes a political developmemt stressing the desireability of increased home ownership and the concept of affordable housing at the outset of the chapter. Leaders from both major parties have promoted home ownership. While there is nothing intrinsically wrong with home ownership, the formulation of political policies designed to make home ownership universal has a utopian air to it and the wisdom of it is highly questionable. Political policies manifested in the form of a revision of credit requirements for home purchases by the Fannie Mae Corporation. The intent being to enable minorities and lower income people to secure mortgages for homes.

Good intentions do not necessarily lead to sound lending policies. Loan standards are as old as loans and protect both the lender and recipients of loans. The housing bust was preceded by the granting of massive amounts of mortgage loans to individuals who would not have qualified for them in the past. The road to easy credit will be detailed in a subsequent blog entry.

Sowell provided useful indicators for the term affordable housing. For individuals it can be viewed as a ratio of mortgage payments to income. For the purpose of regional comparisons it is better viewed as the ratio of median home payments to median income. When sound loan standards are in effect individual applicants for mortgages will be approved and rejected based largely on payment to income ratio data. If payments consume too high a percentage of income not enough will remain for other essential spending like food, clothing, car expenses etc. It is not in the interests of lenders or consumers to have loans granted to those who cannot maintain the payments. We can see from the events of recent history that it is also not in the interests of the American economy as a whole to encourage unsound lending practices.

Sowell correctly pointed out an implicit assumption that has seeped into American political policies i.e. the belief that the government should ensure that home ownership is affordable. That view along with the related belief that there existed a shortage of affordable housing prompted calls for federal intervention. It's essential to understand the actual causes for housing problems in some localized areas of the United States so that effective solutions can be fashioned. It is also imperative for the economic health of this nation that people understand that skyrocketing home prices were not prevalent throughout this nation but rather tended to be localized in regions where government land use policies severely impacted real estate values.

Reference:

The Housing Boom and Bust by Thomas Sowell; Published by Basic Books; Copyright 2009; Chapter 2, Pages 30-36.

Endocytosis in Nature Reviews Molecular Cell Biology

2009-09-12T13:26:00.000-07:00

Nature Reviews Molecular Cell Biology (doi:10.1038) has an edition devoted to endocytosis. There is a nice little introduction to the topic at the website. It notes that endocytosis is associated with numerous functions. These functions include cell adhesion and migration, receptor signalling, nutrient uptake, pathogen entry and cell polarity. Extracellular molecules absorbed through endocytic membrane trafficking need to undergo a sorting process. As stated the different "endocytic processes can be distinguished by the size of the vesicle formed, their cargo and the machineries involved." Origin of life theories often refer to the tendency of lipids to self-assemble as evidence for some kind of ancient proto-cell membrane; one apparently lacking trafficking functions. The linked article notes that "selection of cargo by adaptor proteins is considerably more complex than initially anticipated." Is this the type of process that nature can forego entirely or even tolerate at some sort of very suboptimal level? Maybe, but it looks like the kind of topic a science fiction writer should develop.