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Sunday, 5 September 2021

And still yet more primeval tech v. Darwin.

 Hierarchical Systems in Biology — DNA Packaging

Walter Myers III

Late last year Discovery Institute Research Coordinator Brian Miller asked me about hierarchical systems in biological organisms and how they relate to computer systems. I hadn’t thought much about it previously. However, that question has gnawed at me over the past few months and there are a couple of interesting cases I have been pondering where I believe there is hierarchical structure in nature that intersects with programmatic constructs. 

The first is the overall organization of biological organisms: how they appear to have a layered approach where structures not only build on top of lower ones, but also within those layers there is composition of various parts that work in concert with other parts. For example, in any complex multicellular animal, cells comprise the smallest unit, then you have groupings of cells into structures such as organs, and then these organs are composed to give rise to the full, working organism. Beyond that, there is the thinking part of an organism that seems to defy being reduced to its physical constituents. I will stop there, but that is grist for a future post.

Hierarchical Nature of DNA

The second case I have been thinking about for some time, which is my subject here, is the hierarchical nature of the helical DNA molecule within the cell that carries the genetic instructions to build proteins that perform the work of the cell. It is truly remarkable to see 1) how such a large volume of information can be packed into so little space with its “supercoiled” architecture, 2) the degree to which this information is compressed and packaged within the nucleus of the cell, and 3) how it can be precisely unpackaged where needed to access the instructions for any new protein the cell needs for continued operation. As we will see, it is the chromosome that represents the highest order of DNA compression and organization, containing an organism’s entire genetic content, counted in the number of chromosome pairs. For example, humans have 23 chromosome pairs with one of each of the 23 pairs contributed by the parents, totaling 46 chromosomes.

Advanced life forms, such as humans, dogs, and whales, have what are called eukaryotic cells. Eukaryotic cells, unlike prokaryotic cells such as bacteria, contain a nucleus that stores and protects the genetic material, DNA, which is “condensed” (i.e., packaged) into chromosomes. To get an idea of just how condensed DNA is, inside each and every one of the 30 to 40 trillion cells (excluding bacteria and reproductive cells) that make up a human, if you were to stretch the 3 billion base pairs of DNA end to end, its length would be about two meters. Yet when fully packaged inside the nucleus of a cell (generally during cell division), the 3 billion base pairs in each cell fit into a space just 6 microns (.000006 meters) across. The nucleus itself is about 10 microns (.00001 meters) in diameter, providing ample room for DNA to be unpackaged as needed, as in between cell division chromosomes generally exist in a more diffused state in essential regions to enable faster access for replication or transcription. This is somewhat like the concept of memory caching in computer systems to speed up programs by avoiding slower disk reads for frequently used data. Generally, if a gene is completely packed away, then it will most likely not be expressed (i.e., transcribed and translated into a protein). This makes sense because each of the different cell types in an organism (e.g., muscle, skin, endothelial, nerve, etc.) requires only a small subset of the full set of available proteins coded in the genome.

Carefully and Ingeniously

So how do you package one meter of information content into a space 1/100,000 that size? Very carefully and quite ingeniously. The storage of DNA is very much like hierarchical file systems on Windows and Linux desktop computers compressed into a .zip file. In the same manner that there are folders within folders within folders in a desktop computer, with the actual files at the terminal level, individual genes within a DNA molecule are equivalent to “files” that in this case specify the building of a protein needed for the cell to function. DNA packaging is far more complex, however, with several levels of packaging into a highly compressed and compact structure called chromatin. Essentially, there are three orders of DNA packaging: the first order is the nucleosome, the second order is the solenoid fiber, and the third order is the scaffold loop chromatids chromosome. The diagram below demonstrates the levels of packaging.

Image credit: EreborMountain/Shutterstock.com.

The first level of packaging of DNA is where the double-stranded DNA is wrapped around spools of histone, a family of positively charged proteins that function primarily in packaging DNA, to form nucleosomes, creating the appearance of “beads” on a string. The nucleosomes themselves are then coiled into a 10 nm (10 billionths of a meter) fiber. Each nucleosome “core” consists of eight histone molecules. The nucleosomes are then further folded into the second order supercoiled solenoid fiber, which is 30 nm in width. The third order is the forming of looped domains of solenoid fibers that average 300 nm in width which are then further compressed down to 250 nm to form chromatin fiber. The chromatin fibers are further folded into 700 nm chromatids, and finally we have the highest order of structure that forms the characteristic shape of a chromosome which is 1400 nm in width as seen above. Thus, the general order of packaging is:

DNA → nucleosome → solenoid → chromatin fiber → chromatid → chromosome

A “Chicken and Egg” Problem

It is hard to fathom that such a highly complex, hierarchical mechanism of information storage on a microscopic scale could come about purely by chance, which more importantly demonstrates a clear case of the classic “chicken and egg” problem. This complex, highly orchestrated packaging model, coordinated by the machinery of enzymes (topoisomerases) and various types of histones that are proteins themselves coded in DNA, must have come prior to DNA and prior to the random variation mechanism of evolution itself. The DNA packaging model is programmed with the knowledge of what regions of the chromosome to keep tightly supercoiled and what regions to keep more loosely packed to aid in DNA transcription. Moreover, if a region needed for transcription is supercoiled, it will unwind that region and compensate for the unwinding with a compensating supercoil in a prior region. Thus, there is an astounding process of coordination taking place within the process of transcribing DNA.

Interestingly, there are companies that recognize the genius of DNA and its packaging model who are investigating using DNA molecules as a means of creating molecular-level archival data storage to solve the problem of an ever-increasing amount of digital data that is surpassing the amount of physical storage available using modern magnetic and optical media. For example, tech giant Microsoft is currently engaged in this research, noting the following on their website: “Using DNA to archive data is an attractive possibility because it is extremely dense (up to about 1 exabyte per cubic millimeter) and durable (half-life of over 500 years).” When one considers the fact that the world’s finest software engineers look to the DNA packaging topology to dramatically increase storage capability by orders of magnitude, it is reasonable to conclude that the packaging and processing of DNA is the product of a purposeful designer with a degree of engineering knowledge simply unmatched by humans.

Who then is this God and Father who is above all?

  Ephesians4:6 NASB "one God and Father of all who is over all and through all and in all."



One of the main reasons nontrintarian Christians feel compelled to reject the doctrine of the holy trinity is that it involves the same oft repeated seductions to a free lunch common to all poorly conceived philosophies.To give an example if the trinity doctrine as commonly explained by mainstream churches is true then manifestly no member of the trinity can be "over all" since not only would there be at least two others who are equal in divinity but there would be one (i.e the totality of the Godhead) who/which? would be greater than any single member.The trinity itself/himself? would alone be over all,The God,The most high,the only true God etc.
 Yet the scriptures repeatedly speak of the father alone as the most high,Ho theos i.e the God,the only true God,and as being over all including Christ.
The other purported members of the trinity are spoken of as being of God i.e subject to God so that Jesus is Son of The God(not merely the father) and never God the son,The spirit is the spirit of God(not merely the father or the son) and never as God the spirit. The Father by contrast is always the God the father and never the Father of the God clearly then the Father is the God who owns, sustains and controls the son and the spirit. The father's name alone in scripture is ever referred to as the sacred/holy name hence our lord prayed that YOUR (second person singular possessive),not our name be hallowed/sanctified.
 According to the words of our Lord and saviour Jesus the messiah the time is at hand for all seeking the approval of the one true God to reject this particular seduction to a free lunch and turn to the father i.e Jehovah/yahweh God as the one true God.

John4:23NASB "“But an hour is coming, and now is, when the true worshipers will worship the FATHER in spirit and truth; for such people the Father seeks to be His worshipers"

Seeking a straight answer from Darwinists.

 Can someone outline for me a stepwise Darwinian style  model of the emergence of sexual reproduction. Bearing in mind that any trial that does not succeed on its first attempt effectively resets the experiment to zero.

Lee Kuan Yew: an overview.

 Lee Kuan Yew (born Harry Lee Kuan Yew; 16 September 1923 – 23 March 2015), often referred to by his initials LKY, was a Singaporean statesman and lawyer who served as Prime Minister of Singapore from 1959 to 1990, and is recognised as the nation's founding father. He was one of the founders of the People's Action Party, which has ruled the country continuously since independence.


Lee was born in Singapore during British colonial rule, which was part of the Straits Settlements. He attained top grades in his early education, gaining a scholarship and admission to Raffles College. During the Japanese occupation, Lee worked in private enterprises and as an administration service officer for the propaganda office. After the war, Lee initially attended the London School of Economics, but transferred to Fitzwilliam College, Cambridge, graduating with starred-first-class honours in law in 1947. He became a barrister of the Middle Temple in 1950 and returned to Singapore, and began campaigning for Britain to relinquish its colonial rule.

Lee co-founded the People's Action Party in 1954 and won his first seat in the Tanjong Pagar division in the 1955 election. He became the de facto opposition leader in the legislature to chief ministers David Marshall and Lim Yew Hock. Lee led his party to its first electoral victory in the 1959 election, and was appointed as the state's first prime minister. To attain complete self-rule from Britain, Lee campaigned for a merger with other former British territories in a national referendum to form Malaysia in 1963. Racial strife and ideological differences led to Singapore's separation from the federation to become a sovereign city-state in 1965.

With overwhelming parliamentary control at every election, Lee oversaw Singapore's transformation into a developed country with a high-income economy within a single generation. In the process, he forged a system of meritocratic, highly effective and anti-corrupt government and civil service. Lee eschewed populist policies in favour of long-term social and economic planning. He championed meritocracy and multiracialism as governing principles, making English the lingua franca to integrate its immigrant society and to facilitate trade with the world, whilst mandating bilingualism in schools to preserve students' mother tongue and ethnic identity. Lee stepped down as prime minister in 1990, but remained in the Cabinet under his successors, holding the appointments of senior minister until 2004, then minister mentor until 2011. He died of pneumonia on 23 March 2015, aged 91. In a week of national mourning, about 1.7 million Singaporean residents as well as world leaders paid tribute to him at his lying-in-state at Parliament House and community tribute sites.

Lee has often been considered as a highly oppressive dictator and a stalwart supporter of the so-called Asian values, which espouses constant obedience to the government or face severe consequences such as caning and even the death penalty. Lee's rule was often criticised by observers from the liberal democracies of the West in response. Critics had also accused him of severely curtailing press freedoms, limits on public protests, restricting labour movements from strike action, and bringing defamation lawsuits any political opponents in his way.