Methylation – Focusing the Effects of Cytosine Deamination or a new coincidence to Darwinism?

November 6, 2009

Another stunnig article from Mike GENE.. He hunts ”the Duck” again..

Mike GENE

Back around 2002, I noted that the genetic code appears to funnel one of the most common  base pair substitutions, the C-to-T transitions caused by deamination of the cytosine.  Put simply, codons containing a C specified a wide range of amino acids, but when that C is converted to T, the new set of codons all converge on the most hydrophobic amino acids.  The original analysis is found here.

To see this for yourself, the figure below represents a hydrophobicity scale for the 20 amino acids based on 47 published attempts to quantify hydrophobicity:

Source

Now consider the effect of cytosine deamination using this scale:

Scale on left are the amino acids coded for by C-containing codons which is converted to scale on right by the deamination of those cytosines.

Front-loading Hedgehog

Mike GENE

The hypothesis of front-loading continues to gather traction.  Consider this description of the Hedgehog signaling pathway:

In a growing embryo, cells develop differently in the head or tail end of the embryo, the left or right, and other positions. They also form segments which develop into different body parts. The hedgehog signaling pathway gives cells this information that they need to make the embryo develop properly. Different parts of the embryo have different concentrations of hedgehog signaling proteins. The pathway also has roles in the adult. When the pathway malfunctions, it can result in diseases like basal cell carcinoma. [1]

The hedgehog signaling pathway is one of the key regulators of animal development conserved from flies to humans. The pathway takes its name from its polypeptide ligand, an intercellular signaling molecule called Hedgehog (Hh) found in fruit flies of the genus Drosophila. Hh is one of Drosophila’s segment polarity gene products, involved in establishing the basis of the fly body plan. The molecule remains important during later stages of embryogenesis and metamorphosis.

So here we have a circuit that is essential to the development of metazoan body plans.  How in the world could we front-load this information into a single-celled organism?

EVER SINCE DARWIN

Mustafa Ajlan ABUDAK

This book is the one of the best crtical thinking over blind Darwinism. It has very clear expression on what is the evolution of Darwin. The book tells us our misunderstandings  (I mean for those who are out of field ) and even expert scientists misleadings about evolution and why evolution codes may mean very different things in social life. Especially on these days on Darwın 200 this book must be re-examined by all of whom are interested in evolution and Darwin. Gould draws interesting picture for layman about evolution with words of related evo-sciences.

It is a sure thing that Darwin was a great scientist who formulized the grey scale rules in nature to form designs .What matters here, this is design by chance or design by intelligence . As it seen pure ” Chance” has potential to form something but to do this, chance needs potential in matter to expose design or design -like features (it is meaningles to ping if there is no responder) which must be pre-loaded inside to unpack later in process of evolution and serve as the modulator of the consistency and the stability of gene pool to its habitat.

Steve Fuller’s lecture on ID

Biomimetics: Design by Nature or naturally designed by…

What has fins like a whale, skin like a lizard, and eyes like a moth? The future of engineering.

By Tom Mueller

One cloudless midsummer day in February, Andrew Parker, an evolutionary biologist, knelt in the baking red sand of the Australian outback just south of Alice Springs and eased the right hind leg of a thorny devil into a dish of water. The maneuver was not as risky as it sounds: Though covered with sharp spines, the lizard stood only about an inch high at the shoulder, and it looked up at Parker apprehensively, like a baby dinosaur that had lost its mother. It seemed too cute for its harsh surroundings, home to an alarmingly high percentage of the world’s most venomous snakes, including the inland taipan, which can kill a hundred people with an ounce of its venom, and the desert death adder, whose name pretty well says it all. Fierce too is the landscape itself, where the wind hissing through the mulga trees feels like a blow dryer on max, and the sun seems three times its size in temperate climes. Constant reminders that here, in the driest part of the world’s driest inhabited continent, you’d better have a good plan for where your next drink is coming from.

Go on reading this interesting article from NG

Mike Gene hit the target again from 12.In The Design Matrix pages 89-99

The more we advanced in technology, the more we can detect the design and benefit from…

Front-loading with Homeodomains by Mike Gene

 ”As the new data comes , undirected fabl of Darwinian evolution becomes more and more tricky misinformation of the materialism.This article belongs to my most favourite researcher, Mike Gene who works on directed evolutionary processes called front-loading. Here is the latest article on him. You had better visit his site ( the design matrix ) to learn more about the concept of fron t loading.”

Mike GENE

For years, I have been trying to flesh out the conceptualization of front-loading evolution at the origin of life. A working hypothesis has been that the first cells (uni-cellular life forms) were front-loaded with information that would facilitate the evolution of multi-cellular life. One possible candidate for such front-loaded ‘information’ would be the homeodomain proteins. These proteins play essential roles in metazoan development and are considered part of the developmental toolkit as outlined by biologist Sean Carroll.

A few months ago, a study was published that outlines data and arguments that perfectly resonate with my front-loading views. Let’s have a look.

The study is Homeodomain proteins belong to the ancestral molecular toolkit of Eukaryotes, published by French researchers, Romain Derelle, Philippe Lopez, Herve´ Le Guyader, and Michael Manuel. It was published in the June, 2007 issue of Evolution & Development (9:212–219). Feast your eyes on the abstract:

Flagellum Challenges Darwin’s chances

Keiichi NAMBA
Professor, Graduate School of Frontier Biosciences, Osaka University

INTERVIEW 

Nature created a rotary motor with a diameter of 30 nm. Motility of bacteria, such as Salmonella and E. coli with a body size of 1 ~ 2 microns, is driven by rapid rotation of a helical propeller by such a tiny little motor at its base. This organelle is called the flagellum, made of a rotary motor and a thin helical filament that grows up to about 15 microns. It rotates at around 20,000 rpm, at energy consumption of only around 10-16 W and with energy conversion efficiency close to 100%. Prof. Namba’s research group is going to reveal the mechanism of this highly efficient flagellar motor that is far beyond the capabilities of artificial motors. (Such as some F1 high engineering motors have recently reached below this rpm like BMW’s 19250-500)

The flagellum is made by self-assembly of about 25 different proteins. The rotor ring made of protein FliF is the first to assemble in the cytoplasmic membrane. Then, other protein molecules attach to the ring one after another from the base to the tip to construct the motor structure. After the motor has been formed, the flagellar filament, which functions as a helical propeller, is assembled. Precise recognition of the template structure by component proteins allows this highly ordered self-assembly process to proceed without error. The flagellar filament is made of 20,000 to 30,000 copies of flagellin polymerized into a helical tube structure. Flagellin molecules are transported through a long narrow central channel of the flagellum from the cell interior to the distal end of the flagellum, where they self-assemble in a helical manner by the help of a cap complex. The cap is pentameric complex made of HAP2 and has a pentagonal plate and five leg domains, whose flexible stepping movements accompanied by rotation of the whole cap is the key mechanism to promote the efficient self-assembly of flagellin molecules by preparing just one binding site of flagellin at a time and guiding the binding.

 More.. 

On ”A simpler Origin for Life”

Robert Shapiro is one of the greatest scientist on DNA chemistry. He has over 125 publications and many scientific articles and his last article entitled as ” A simpler Origin for Life” He amazingly describes why the Darwinian manner of evolution is invalid about explanining life on earth.He confessed that Darwinian scoptoma is totally improbable and impossible when we take mathematical probalities of origins of molecular life into consideration.He put forward polished claim called small molecules rooted back to Oparin, Russian scientist. He explained his theory with same intruments within the Darwinian toolbox.As everyone knows R.Dawkins loves to use those grammatical intruments when he tells his fairy tales about evolution.They are such as ; If…., may have, might have, colud have been, etc.. but R.Shapiro is maybe the one and only scientist ,being honest about Darwinian evolution from the materialist camp.His works lead us cross examining the facts  which science has discovered about molecular life and evolution within last decades.

Here is his latest article on Sciam

Irreducible Complexity And Darwinian Pathways

 

 Irreducible Complexity And Darwinian Pathways
Guest response to article by R.H. Thornhill and D.W. Ussery
“Mike Gene“

ARN Forum
June 16, 2000

It’s official. Behe’s concept of irreducible complexity (IC) has found itself in the peer-reviewed scientific literature. Ironically, it was introduced by two critics of ID attempting to formulate non-teleological mechanisms for spawning IC. The article is: Thornhill, R.H., Ussery, D.W. 2000. “A classification of possible routes of Darwinian evolution.” J. Theor. Bio. 203: 111-116.

First of all, this article shows that Behe’s work has indeed contributed to science. Thornhill and Ussery (T&U) write:

“However, the more theoretical question about the accessibility by Darwinian evolution of irreducibly complex structures of functionally indivisible components, if such exist, has not been thoroughly examined.One factor hampering examination of the accessibility of biological structures by Darwinian evolution is the absence of a classification of possible routes. A suggested classification is presented here.”