8/13/15

Public Domain Gene Sequencing

GAP4 is a free Staden gap4 assembly editor available for linux software installation. It does make me wonder, not being a biologist, where all of this broadly available technology of genetic morphing leads-I suppose in a plethora of wild directions whereby do-it-yourselfers make lifeforms that might survive on exoplanets and moons and that think and play chess better than stockfish.

Well, that might be looking a little ahead. Perhaps Al Qaeda will be playing about with bio-war prospects until they get grad degrees in the field. One of these days someone will write out cycle cell anemia and skin cancer from genetic traits I suppose even adding some sort of patch for existing people. Even so there are a number of distopian possibilities with genetic war and tomfoolery where people get under whatever barriers are in place to Doctor Morrowing by whatever corrupt government one is compelled to be persecuted by.

The following is what is said by the producer about the install...

"Staden is a fully developed set of DNA sequence assembly (Gap4 and Gap5), editing and analysis tools (Spin).

Gap4 performs sequence assembly, contig ordering based on read pair data, contig joining based on sequence comparisons, assembly checking, repeat searching, experiment suggestion, read pair analysis and contig editing. It has graphical views of contigs, templates, readings and traces which all scroll in register. Contig editor searches and experiment suggestion routines use confidence values to calculate the confidence of the consensus sequence and hence identify only places requiring visual trace inspection or extra data. The result is extremely rapid finishing and a consensus of known accuracy.

Pregap4 provides a graphical user interface to set up the processing required to prepare trace data for assembly or analysis, and automates these processes.

Trev is a rapid and flexible viewer and editor for ABI, ALF, SCF and ZTR trace files.

Prefinish analyses partially completed sequence assemblies and suggests the most efficient set of experiments to help finish the project.

Tracediff and hetscan automatically locate mutations by comparing trace data against reference traces. They annotate the mutations found ready for viewing in gap4.

Spin analyses nucleotide sequences to find genes, restriction sites, motifs, etc. It can perform translations, find open reading frames, count codons, etc. Many results are presented graphically and a sliding sequence window is linked to the graphics cursor. Spin also compares pairs of sequences in many ways. It has very rapid dot matrix"

8/11/15

Natural Genocide from Progressives in Social Evolution

In a way, the post-Columbian genocide of American aboriginals was a natural social evolution rather than a genocide by intention.Why did deforestation happen to much of the world, why did global warming and mass species extinction happen as population grew and technology developed? It wasn't really by design. In that era people fought tribally-even in Europe, under royal leaders generally. Disease, human migrations and displacement annihilated those in the path of progress and some of those progressives too. Genocide can occur by design, yet they can also just evolve because of human social circumstances.

A better number for post-Columbian loss of aboriginal life in the Western hemisphere as a result of disease, slavery, murder, displacement and so forth has been set at 16 million. The average life span on Earth was fewer than 25 years. Bubonic plague had killed of 2/3rds of European population in the preceeding centuries. Mongols had invaded Russia and Europe to Novogorod and south to Ukraine. In 1500 the entire world population was about 425 million. Few were literate, many were savages and acted that way in war and peace too like as not. People had different ethics. They had poor diplomacy. They did not communicate well. It might be less painful to die in war than from untreated cancer. People killed a lot and didn't wash their hands with soap either. They had little prospect for a priesthood of the laity on Sundays with hired-gun sermonizer stars performing at Wens night church meetings. I think that its a hard thing to consider the conquistadores as representative Christians-many were criminals, yet they were very tough institutionally after fighting to get rid of Muslims half a millennium in Spain. Even Columbus was sent back to Spain in chains. Aboriginals were not all peace and love children-they had human sacrifice, cannabalism and slavery of other tribes. They would use a knife to cut POWs so they had to piss like women. Most of the depopulation occurred in Mexico and today's Latin American and Caribbean basin-not in the U.S.A. or Canada. Depopulation loss of life in the area that is the U.S.A. was 2-3 million, from all, including unintentional causes (such as smallpox). Most of the aboriginals lived in Mexico and South America. Entire civilizations were wiped out by disease at first biological contact. As that of El Dorado. https://www.youtube.com/watch?v=0Os-ujelkgw a lost civilization https://www.youtube.com/watch?v=IScmhWjGUl4 https://www.youtube.com/watch?v=YxNyM6XPZ0M

8/8/15

Toward a Level III Civilization

Human beings are the only animal that is harmful to the environment. That is of all life on Earth humans are the only ones specializing in the gross destruction of habitat such that all other life declines. Contemporary social problems regarding environment extend far beyond global warming; since humanity ate of the tree of knowledge learning how to manufacture implements to destroy things they have been able to increase their killing power far beyond their natural biological capacity without the use of tools, chemicals and so forth.

Killing things to get food and comfort is natural enough in nature. Human beings however have learned to kill the environment or consume it far beyond their non-tool aided ability. One may regard that as a natural intellectual transition from the state of innocent animals to animals with larger, thinking brains able to kill things and pile up comforts in health, housing and sensuality, yet that spiritually dead condition is a kind of Satanic animal status creating the greatest mass extinction in world history that is a result of sentient power.

Human beings need to transition to a Level Three intellectual condition . Level I is that of animals, Level II is that of animals that use tools to kill proficiently and manufacture comforts. Level III is a spiritually regenerated condition with grace from the Lord and moral economics informed by right use and conservation of life instead of just consuming and/or killing it. A level III civilization creates and increase life rather than destroy it.


If humanity remains like plain animals that consume with capacity increased with tool and technical invention without spiritual regeneration not only is life on Earth likely to be wiped out, the lost Level I souls also have an eternity in hell ahead of them. A Level III civilization should be one with the saved bringing life to barren planets and finding a way that all human beings alive today can share in keeping as many species alive as God has provided to exist on earth, sea and sky.

8/7/15

Another Wild Scenic River Threatened by Development

Upstream development of mining and dwellings threatens then long-term health of the wild Stikine River of S.E. Alaska. Canadian mine tailings waste waters have already spilled into the river that ways a primordial avenue for Athabaskan peoples to settle S.E. Alaska 7000 years ago. At the river delta a great battle between Tlingits and oceanic Indians developed that a winning Tlingit leader named Gush X'een used to take the defeated Tsimshian clan's leader title of  Sheiyksh (Chief Shakes). Without International protection the heritage river will fall victim to thoughtless waterfront developers and miners that make a mess of metallic water pollution lasting for thousands of years.

https://en.wikipedia.org/wiki/Chief_Shakes

Like most other American rivers the Stikine is probably destined to become a polluted drainage ditch with industrial pollution and subdivisions crowding out the forest and wildlife along its shores. Formerly 100lb king salmon returned to the River. In the salmon derby held annually at Wrangell it is rare to have even a 40 lb. champion. Over-fishing harvesting the big fish has left just runts to take over the water. Bear and whale are plinking targets of speed boaters with fish finders and hearts the size of intellects.

It is well known that human beings are dominated by uncreative, thoughtless consumers of natural resources that are something like five or six foot ants consuming what God has provided without much consideration given to economic resource efficiency. The hive queens demand top quality resource nectar for their progeny and sell the body parts of aborted infants to harvest additional profit. The mindless atheists seeking after sensual gratification without spirit take down anyplace healthy and convert it into quickest, dirtiest profits possible. If the Stikine River is to be saved from the usual doom the upstream Canadian mines will need to be halted and the entire River made into a world wild River Refuge-Park extending from the delta near Wrangell Alaska to the Cassiar Highway in the Canadian interior. The entire drainage system is vast and of far more future value in a wild condition to humanity than the mindless aggression against the few remaining wild regions the U.S.A. has.





sin vs holiness (video)

8/6/15

Jesse Benton-Not Rand Paul, Indicted

A former short-time PAC chair supporting Rand Paul's candidacy was indicted evidently according to a 'Daily Beast' article by Olivia Nazzi that ran with the misleading statement  "Rand Paul Indicted"
"

"Rand Pal Indicted; Cries Conspiracy"

http://www.thedailybeast.com/articles/2015/08/05/rand-paul-super-pac-head-indicted.html

Rand Paul must have discovered for himself something irregular about the fellow since he moved on rather quickly. Paul and Donald Trump are the main Republican American candidates not bought and paid for by global corporatism. It is not surprising that the media dislike Paul since he is not rich like Trump, who is at least respected for being competent and pragmatist on global economics. President Obama send Vladimir Putin a load of sweet Cuban sugar cane politically speaking when he opened diplomatic relations with the Castro regime. Paul would perhaps accomplish a similar mission with Americans giving them a chance to develop free of so much outsourcing of opportunity and wages to China.

It makes little sense to force people to retire or go on disability instead of working at a fair wage. There are fewer people working in the U.S.A. now than in 1979.

"Direction to Unconverted, Graceless Sinners, for the Attaining of True Saving Grace"

Richard Baxter was something of a social philosopher anticipating Pascal and James' wager besides understanding human beings and their nature rather well. 
II found that a .txt file of Baxter's books, at least on ethics, is available on-line. So I downloaded it and found it full of typo errors that are probably a result of taking the pdf google photocopy version of the 1825 publication in the Harvard Library and running it through a photo-into-text program that misunderstood many words/spellings. Even so it is a very helpful text and potentially can be corrected by someone with the time to do so. http://digitalpuritan.net/richard-baxter/ text file with typos and computer misniterpretations One need only compare the two documents (PDF & TXT) and make the corrections. If the .txt file was corrected it could be also given a modern font and made into a PDF file with proper headers (style 1-3) that enable easy index subject navigation. Since Baxter is actually good reading it would be worth the time to produce a contemporary presentation of 'Practical Divinity'. Following is an example of a corrected version (with minor updates in word usage though without styles headers ) from Baxter's Practical Divinity... quote- "Direction to unconverted, graceless Sinners, for the attaining of true saving Grace. If ungodly, miserable sinners were as few, as the devil and their self-love would make themselves believe, I might forbear this part of my work as needless. For the whole need not the physician, but the sick. If you go into twenty families, and ask them all. Whether any of them are in an unsanctified state, unrenewed and unpardoned, and under the wrath and curse of God? you will meet with few that will not tell you, they hope it is better with them than so; and thou they are sinners, as all are, yet that they are repenting, pardoned sinners. Nay, there is scarce one of many of the most wicked and notoriously ungodly, but hope they are in a penitent, pardoned state. Even the haters of God will say they love him ; and the scorners at godliness will say that they are not ungodly; and that it is but hypocrisy and singularity that they deride:: and it were well for them, if saying so would go for proof, and he that will be their judge would take their words. But God will not be deceived, though foolish men are wise enough to deceive themselves. Wickedness will be wickedness when it hath clothed itself with the fairest names : God will condemn it when it hath found out the most plausible pretences and excuses. Though the ungodly think to bear it out in pride and scorn, and think to be saved by their hypocritical lip-service, as soon as the most holy worshippers of the Lord, yet "shall they be like chaff which the wind driveth away: they shall not be able to stand in judgment, nor sinners in the congregation of the righteous*." And if God know better than foolish men, then certainly the flock is little to whom the "Father will give the kingdom'*." And "wide is the gate, and broad is the way that leadeth to destruction, and many there be that go in thereat": because strait is the gate, and narrow is the way which leadeth unto life, and few there be that find it." When Christ was asked, "Lord, are there few that be saved?" he answered, "Strive to enter in at the strait gate ; for many I say unto you, will seek to enter in, and shall not be able." But, alas! we need no other information than common experience, to tell us whether the greatest part of men be holy and heavenly, and self-denying; that seek first the kingdom of God and his righteousness, and love God above all, and will forsake all they have for the sake of Christ, and undoubtedly none but such are saved; as you may see Heb. xii. 14. Matt. vi.20, 21. 33. Seeing then the godly are so few, and the ungodly so many; and that God will take nothing for holiness that is not such indeed ; and seeing it is so terrible a thing to any man that hath his wits about him, to live one day in an unconverted state, because he that dieth so, is lost for ever; methinks it should be our wisdom to be suspicious of ourselves, and careful lest we be deceived in so great a business, and diligent in searching and examining our hearts, whether they are truly sanctified or not ; because it can be no harm to make sure work for our salvation; whereas presumption, carelessness, and negligence, may betray us to remediless misery and despair. I do not here suppose the reader to have any such acquaintance with his heart, or care of his salvation, or obedient willingness to be taught and ruled by Jesus Christ, as is proper to those that are truly sanctified ; for it is ungodly persons to whom I am now speaking. And, yet, if I should not suppose them to have some capacity and disposition to make use of the Directions which I give them, I might as well pass them by, and spare my labour. I tell thee therefore, reader, what it is that I presuppose in thee, and expect from thee, and I think thou wilt not judge me unreasonable in my suppositions and expectations. 1. I suppose thee to be a (hu)man, and therefore that thou has reason and natural free-will (that is, the natural faculty of choosing and refusing), which should keep thy sensitive appetite in obedience; and that thou art capable of loving and serving thy Creator, and enjoying him in everlasting life. 2. I suppose that thou knowest thyself to be a (hu)man; and therefore that thy sensitive part, or flesh, should no more rule thee, or be ungoverned by thee, than the horse should rule the rider, or be unruled by him ; and that thou understandest that thou art made on purpose to love and serve thy Maker, and to be happy in his love and glory for ever. If thou know not this much, thou knowest not that thou art (hu)man, or else knowest not what a (hu)man is. 3. I suppose thee to have a natural self-love, and a desire of thy own preservation and happiness; and that thou has no desire to be miserable, or to be hated of God, or to cast out of his favour and presence into hell, and there to be tormented with devils everlastingly: yea, I will suppose that thou art not indifferent whether thou dwell in heaven or hell, in joy or torment; but would fain be saved and happy; whether thou be godly or ungodly, wise or foolish; I will be bold to take all this for granted: and I hope in I this i do not wrong thee. 4. I suppose thee to be one that knowest that thou did not make thyself; nor give thyself that power or wisdom which thou has; and that he that made thee and all the world, must needs be before all the world; and that he is eternal, having no beginning (for if ever there had been time when there was nothing, there never would have been any thing; because nothing can make nothing); and I suppose thou dost confess that all the power, and wisdom, and goodness of the whole creation set together, is less than the power, and wisdom, and goodness of the Creator; because nothing can give more than it hath to give. I suppose, therefore, that thou dost confess that there is a God ; for to be eternal, infinite Being, and the most powerful, wise, and good and the first cause of all created being, and power, wisdom. and goodness, this (with the subsequent relations to the creature) is to be GOD. If thou wilt deny that there is a God. thou must deny that thou art a (hu)man, and that there is any (hu)man, or any being*. 5. I suppose thou knowest that God, who gave a being unto all things, is by this title of creation, the absolute Owner or Lord of all : and that he that made the reasonable creatures, with natures to be governed, in order to a further end, is by that title, their supreme Governor; and therefore hath his laws commanding duty, and promising reward, and threatening punishment; and therefore will judge men according to these laws, and will be just in judgment, and in his rewards and punishments. And that he that freely gave the creature its being, and all the good it hath, and must give it all that ever it shall have, is the Father or most bountiful Benefactor to his creatures. Surely I screw thee not too high in supposing thee to know all this; for all this is no more than that there is a God. For he is not God, if he be not the creator, and therefore our owner, our ruler, and benefactor, our absolute Lord, our most righteous governor, and our most loving father, or benefactor. 6. I suppose therefore that thou art convinced, that God must be absolutely submitted to, and obeyed before all others in the world, and loved above all friends, or pleasures, or creatures whatsoever. For to say, ' He is my Owner,' is to say, ' I must yield myself to him as his own:' to say, 'I take him for my supreme Governor,' is to say, that 'I will absolutely be ruled by him:' and to say, 'I take him as my dearest Father or chief Benefactor,' is to say, that 'I am obliged to give him my dearest love, and highest thanks:' otherwise you do but jest, or say you know not what, or contradict yourselves, while you say, 'He is your God.' 7. I suppose that thou art easily convinced, that in all the world there is no creature that can shew so full a title to thee as God ; or that hath so great authority to govern thee, or that can be so good to thee, or do so much for thee, as God can do, or hath done, and will do. if thou do thy part; and therefore that there is nothing to be preferred before him, or compared with him in our obedience or love: nor is there any that can save us from His justice, if we stand out against him. 8. I suppose that as thou knowest God is just, in his laws and judgments, so that he is so faithful that he will not, and so all-sufficient, that he need not deceive mankind, and govern them by mere deceit: this better beseems the devil, than God: and therefore that as he governeth man on earth by the hopes and fears of another life, he doth not delude them into such hopes or fears: and as he doth not procure obedience by any rewards or punishments in this life, as the principal means (the wicked prospering, and the rest being persecuted and afflicted here), therefore his rewards or punishments, must needs be principally hereafter in the life to come. For if he have no rewards and punishments, he hath no judgment ; and if he have no judgment, he hath no laws (or else no justice); and if he have no laws (or justice), he is no governor of man (or not a righteous governor) ; and if he be not our governor (and just), he is not our God ; and if he were not our God, we had never been his creatures, nor had a being, or been men'. 9. I suppose thou knowest that if God had not discovered what he would do with us, in the life to come,. yet man is highliest bound to obey and love his Maker, because he is our absolute Lord, our highest ruler, and our chief benefactor; and all that we are or have is from him. And that if man be bound to spend his life in the service of this God, it is certain that he shall be no loser by him, no not by the costliest obedience that we can perform ; for God cannot appoint us any thing that is vain ; nor can he be worse to us than an honest man, that will see that we lose not by his service. Therefore that God for whom we must spend and forsake this life, and all those pleasures which sensualists enjoy, hath certainly some greater thing to give us, in another life. 10. I may take it for granted at the worst, that neither thyself, nor any infidel in the world, can say that you are sure that there is not another life for man, in which his present obedience shall be rewarded, and disobedience punished. The worst that ever infidel could say was, that 'He thinketh that there is no other life.' None of you dare deny the possibility of it, nor can with any reason deny the probability. Well, then, let this be remembered while we proceed a little further with you. 11. I suppose or expect that you have so much use of sense and reason, as to know the brevity and vanity of all the glory and pleasures of the flesh; and that they are all so quickly gone, that were they greater than they are, they can be of no considerable value. Alas, what is time! How quickly gone, and then it is Nothing! and all things then are nothing which are passed with it! So that the joys or sorrows of so short a life, are no great matter of gain or loss. I may therefore suppose that thou canst easily conclude,that the bare probability or possibility of an endless happiness, should be infinitely preferred before such transitory vanity, even the greatest matters that can be expected here; and that the probability or possibility of endless misery in hell, should engage us with far greater care and diligence to avoid it, than is due for the avoiding any thing that you can think to escape by sinning ; or any of the sufferings of this momentary life. If you see not this, you have lost your reason ; that the mere probability or possibility of a heaven and hell, should much more command our care and diligence, than the fading vanities of this dreaming, transitory life. 12. Well, then ; we have got thus far in the clearest light. You see that a religious, holy life, is every man's duty, not only as they owe it to God as their creator, their owner, governor, and benefactor; but also, because as lovers of ourselves, our reason commandeth us to have ten thousandfold more regard of a probable or possible joy and torment which are endless, than of any that is small and of short continuance. And if this be so, that a holy life is every man's duty, with respect to the life that is to come, then it is most evident, that there is such a life to come indeed, and that it is more than probable or possible, even certain. For if it be but man's duty to manage this life, by the hopes and fears of another life, then it must follow, that either there is such a life to come, or else that God hath made it man's duty to hope, and fear, and care, and labour, and live in vain; and that he himself doth tantalize and cheat his creatures, and rule the world by motives of deceit, and make religion and obedience to our Maker to be a life of folly, delusion, and our loss. And he that believeth this of God, doth scarcely believe him to be God. Though I have mentioned this argument in another treatise, I think it not unmeet here to repeat it for thy benefit. 13. And seeing I suppose thee to be convinced of the life to come, and that man's happiness and misery is there, I must needs suppose that thou dost confess, that all things in this life, whether prosperity or adversity, honour or dishonour, are to be esteemed and used as they refer to the life to come. For nothing is more plain, than that the means are to have all their esteem and use in order to their end. That only is good in this life, which tendeth to the happiness of our endless life ; and that ia evil indeed in this life, that tendeth to our endless hurt, and to deprive us of the everlasting good. And therefore no price or motive should hire us to sin against God, and to forfeit or hinder our endless happiness. 14. I may suppose, if thou have reason, that thou wilt confess that God cannot be too much loved, nor obeyed too exactly, nor served too diligently (especially by such backward sinners, that have scarce any mind to love or worship him at all) ; and that no man can make too sure of heaven, or pay too dear for it, or do too much for his salvation, if it be but that which God hath appointed him to do. And that you have nothing else that is so much worth your time, and love, and care, and labour. And therefore though you have need to be stopped in your love, and care, and labor for the world, because for it you may easily pay too dear, and do too much ; yet there is no need of stopping (humanity)men in their love, and care, and labour for God and their salvation ; which is worth more than ever we can do, and where the best are apt to do too little. 15. I also suppose thee to be one that knowest, that this present life is given us on trial, to prepare for the life that shall come after; and that as men live here, they shall speed for ever ; and that time cannot be recalled, when it is gone ; and therefore that we should make the best of it while we have it. 16. I suppose thee also to be easily convinced, that seeing man hath his reason and life for matters of everlasting consequence, his thoughts of them should be frequent and very serious, and his reason should be used about these things, by retired, sober deliberation. 17. And I suppose thee to be a man, and therefore so far acquainted with thyself, as that thou mayst know, if thou wilt, whether thy heart and life do answer thy convictions, and whether they are more for heaven or earth ; and therefore that thou art capable of self-judging in this case. Perhaps you will say, that while I am directing you to be holy, I suppose you to be holy first ; for all this seemeth to go far towards it. But I must profess that I see not any thing in all these suppositions, but what I may suppose to be in a heathen ; and that I think all this is but supposing thee to have the use of thy reason, in the points in hand. Speak freely: Is there any one of all these points that thou canst or darest deny? I think there is not. And therefore if heathens and wicked men deny them in their practice, that doth but show that sin doth brutify them, and that, as men asleep, or in a crowd of business, they have not the use of the reason which they possess, in the matters which their minds are turned from. 18. Yea, one thing more I think I may suppose in all or most that will read this book ; that you take on you also to believe in Jesus Christ, and in the Holy Ghost the Sanctifier, and that the Scriptures are the Word of God, And if you do so indeed, I may then hope that my work is in a manner done, before I begin it: but if you do it but opinionatedly and uneffectually, yet God and man may plead with you the truths which you profess. "-end of quote

After the Space Odyssey (a poem)

  The blob do’ozed its way over the black lagoon battling zilla the brain that wouldn’t die a lost world was lost   An invasion of the carro...