Archive for May, 2010

Genetic ancestry testing

Saturday, May 15th, 2010

Ancestry is about phylogeny : the lineage of ancestor-descendant that every human being manifests. It’s existence is not in question but the validity of the methodologies and the societal implications of this rapidly growing area of personal interest is beginning to be questioned. Today the American Journal of Human Genetics [86(5):661-673] published their report on ancestry genetics testing in which they address these questions. Firstly, ancestral genetic testing has little to do with phylogenic lineages in the sense understood by the palaeontologist i.e. spans > 5 million years. However, genetic testing is relevant to defining the ethno-cultural gamodeme an individual came from; and, how one’s ancestors got to the geographical location a person was born in. Secondly, discussion of genetic ancestry is beginning to move into the tricky area of ethics: this is where a vicious battle could take place, as currently the war between individual and group rights begins to focus at a more general level.

Paternal [Y-chromosome] and maternal [mtDNA] genetic testing can provide phylogenic information about the ancient gamodeme an individual’s ancestors came from. When the information is placed in a relative, as opposed to an absolute, time-scale this is the most general, valid, conclusion that can be made from genetic testing. More specific conclusions are possible where comparisons can be made to a database of many individuals in which the location of origin is known: this was the method used by the pioneers in the field such as Cavalli-Sforza et al.,1994,2001; Wells,2004,2007; and, Sykes,2002, amongst others. Rough absolute time scales are available for this kind of information.

When genetic tests are used for genealogical analysis the results, generally, are quite restricted and can directly link members of only two lineages: those of the fathers paternal grandfather etc., and the mothers maternal grandmother. The methods used can allow reliable conclusions to be derived about ancestry and are useful in determining parentage, and confirming oral and written genealogical hypotheses. The organisation specialises in this kind of analysis.

Between the reliable extremes of ancestral gamodeme and immediate genealogical determination is the gray area where conclusions are tentative and often based upon unsubstantiated hypotheses and conjecture; or, use non-scientific methodologies for data analyses. This gray area is the exciting area because it is open to scientific experimentation: Bryan Sykes’ book “Blood of the Isles” [2006] / “Saxons, Vikings and Celts” [2007] delves into this gray area and is an excellent example of what the gray area is and what can be done within it.

The second area, of ethics, is non-scientific and shows the beginning of intrusion of corporate world into individual choice and freedom with the focus on extracting money for interpreting services. It is a characteristic of American society that professional certification, provided by a non-educational organisation, is often required by law to perform a service. These organisations have often come about by a few individuals who either wish to build a personal empire, or, create a barrier of the kind “we are the knowledgeable and you are not”. Personally, I have always fought against such restrictive techniques because experience has shown that few bodies should have regulatory authority when it comes to knowledge. Most professional bodies do not need, themselves, to provide additional professional training: even though they may require it for continued membership e.g. professional accountants. Additional professional training is the job of independent educational institutions such as trade schools and universities; and, of training programs run under their auspices. Belonging to a body such as the Royal College of Surgeons, or the American Academy of Sciences, or Engineering is recognition of a certain quality of experience and is an obvious guideline when hiring someone for a specific purpose: however, it is up to the individual asking for service to determine whether or not to use a particular person or organisation.  As anyone who has been an expert witness will know, the American legal system does not tolerate incompetent experts: our lawyers are too cunning for that. For government to regulate so that only a member of a professional organisation can legally collect, provide or interpret information is, in my opinion, grounds for insurrection, rebellion and revolution. I have said before: “requiring a bit of paper from a private, non-independent organisation that espouses group superiority is detrimental to our educational system and individual freedom.” We must be vigilant and oppose the development of a system created by lobbying and political ineptitude, that restricts knowledge propagation and encourages financial greed and/or arrogance.

Comment: Professor George F. Hart, 10th, May, 2010.

i I have not yet read the full report so will only comment on the related topics, of interpretation and ethics, of genetic testing.  The following is an interesting related article.

The purpose of life: happiness or usefulness?

Thursday, May 13th, 2010

Notes for a debate on July 24th, 2010.

By Professor  George F. Hart  with contributions by Bill Ross

Any discussion of the purpose of life by a western scientist must include the views of Ayn Rand [1905-1982] and how purpose, group and individual rights, and capitalism impact upon the question. Anne Rand is a persistent character in the lives of Laissez Faire capitalists. She was a Russian philosopher, writer, novelist who wrote “Atlas Shrugged” and developed the hypothesis of objectivism. Her relevance is the important influences she had on capitalistic theoreticians. In her hypothesis of objectivism she expounds:

  1. Reality exists independent of consciousness.

  2. Individual persons are in contact with this reality through sensory perception.

  3. human beings can gain objective knowledge from perception though the process of concept formation and inductive and deductive logic.

  4. The proper purpose of one’s life is the pursuit of one’s own rational self-interest

  5. The only social system consistent with this moral happiness is full respect for individual rights, embodied in pure Laissez Faire Capitalism.

Until recently it was only the last statement I disagreed with, because my world-experience indicated that other economic systems besides capitalism promote individual rights, and allow people to live together within a peaceable social gamodeme. That satisfying one’s own self-interest made a person happy, and this personal happiness was the purpose of life, was logical and acceptable to my personable id. However, upon reflection I realize that I have been happy only very few times in my entire life. Some of these occasions I remember well: when I was married, when each of my three sons was born, when I realized that my grand-daughter would live. Most of the other good occasions were times of satisfaction not happiness: when I was the first student ever to achieve a particular academic standard at Darlington Grammar School, when my wife and I got our first car, when I successfully completed a 350 mile walk up the Wild Coast of South Africa with Patsy-Anne Phillips. [I love the heart-felt, intimate sharing.  Rare amongst humans].With the wisdom that comes with experience I now know that these periods of happiness and satisfaction were self-reinforcing. Self-reinforcing behaviour can arise from the accumulation of experiences and alter future decisions: they affect how I will personally react with reality in the future. Happiness and satisfaction have little to do with the purpose of life and can have evil consequences. Hitler was happy at learning that France had capitulated and set in motion the elimination of more Jewish people [he did not dance a jig as reported – that was a looped movie giving the impression of a jig!]. Is a man allowed to use his strength to bring personal happiness by brutality? The hungry man is free to pursue food but is he allowed to steal and kill if he and his family are destitute and without food. Many would steal and kill for the happiness that food can bring to a starving family. Government regulates to curtail this sort of happiness so that the strong only use their strength in actions that do not intrude upon someone else’s individual rights: the golden rule of the social gamodeme. For a moral person – a person socialized to societal norms – happiness must be achieved without hurting or intruding on others ... but what of the conflict between belief systems. The religious fanatic seeks happiness in perpetuating his belief, in expanding it until it encompasses or eliminates all within its potential grasp by the sword if necessary …. all for the happiness of the mythical concept of heaven; and, in some groups, having sex with a bunch of virgins. Is contentment the quest for a society in which different racial groups are physically separated and one is the inferior to the other as with apartheid? Good points, but again for this discussion I would ask that we define the ‘purpose of life’ for persons living within the social norms of his or her society.  As morality and social norms can be relative, achieving a purposeful life can vary significantly by society. But I will refer to Joseph Cambell once again where he insists that ‘happiness’ is achieved by living and archetypical life.  In other words you can define happiness – or deep satisfaction – as a man if you: prove your courage [rights of passage] to other men, contribute to your community e.g. help kill a buffalo – here you can prove your courage and contribute in one hunt., love a woman, and be loved figuratively and literally, bear  or sire children and …deal with the devastating angst of an unexplained cosmos i.e. adopt a spiritual paradigm.  I recall my finest moments of happiness when I’ve navigated the perilous straits of life and come out the other side with successes in these archetypal areas.  The dramatic successes are best remembered but are tempered by painful memories of battles lost, expectations sashed and inexplicable bouts of disillusionment – the loss of life’s spark. The milieu of life’s highs and lows is romanticized in literature and popular culture and it’s how we ‘process’ our pasts to ‘make the most ‘ of our history.  The low times are not so romantic while we’re living through them.  The self-reinforcing affects of successes carry you through the tough times and give you the courage to try again.  We’re lost when we loose that life-force called confidence.  We have all  lost and regained it a few times.

The liberal institutional democracies [LID's] have a superimposed economic system on the political system, the purpose being to provide a fair distribution of resources so that individuals can pursue their individual quest for happiness. “The role of the government is strictly limited to the enforcement of an individuals right to his own life, liberty and the pursuit of his / her own happiness”. What about sharing, caring and the better well-being of all people? Is the happiness and contentment of the group more important than that of the individual? Whereas, people have an individual right to work for a successful life, they do not have a right to abuse this individual right by becoming increasingly obsessed with power or profit. I am an elitist and believe elitism is an admirable humanity trait in that it recognises that some are better than others in some or many aspects of their ability. However, elitism which fails to include the general good and uses ability to influence and control the lives of others in ways that are not advantageous for the overall cultural gamodeme are not pursuant of the purpose of life. It can lead to sorrow for other people: to the development of an underclass of working poor alienated from happiness, to greed, crime and corruption. So what is the purpose of life? We agree that an elitist, pursuing happiness without regard for his fellow human beings is a dark individual, indeed. Most  societies ostracise such individuals and stab them with the label ‘selfish’ or ‘hedonist’.  Again, if society can successfully socialize their citizens to regard helping others or contributing to society as a good thing, then in their pursuit of happiness they will feel compelled – either innately as Cambell implies – or via social indoctrination to include a social contribution as part of the formula for happiness.  This  is the paradox of the ‘pursuit of happiness’.  It is always interpreted to mean happiness to the exclusion of others, whereas properly socialized individuals will view such a pursuit as a shallow, ultimately empty endeavour.  In effect, a properly socialized citizen puts tremendous value in receiving an acknowledgement that they have contributed to society.  An interesting question is where or not this is innate [part of the human archetypal essence] or an invention of social evolution?

Historically western liberalism is rooted in a faith in human freedom and Locke’s  trinity of natural rights: the right to life, liberty, and property. These rights can provide happiness and contentment but are they connected with the purpose of life? The Declaration of Independence asserts that “men are created equal”; but this is equality only of opportunity, the right for a person to go as far as effort and ability will carry: the right to a meritorious system of political and economic thought. Equality is not equated with the idea that everyone should go equally far, handicapping the elite and the more capable and industrious, and allowing an unlimited support by the State for those who are less successful. The American Constitution does not allow for the elitist to be pillaged to support those of lesser wealth or position. It is the concept of “the purpose of life as individual usefulness” where the quality of a support for the less able or less successful comes from not from the pursuit of happiness.

The 18th century idea of charity generally carried the stigma of inferiority by both the giver and the receiver. We can replace the concept of charity by that of purposeful usefulness. To be relevant is to be counted, to be useful. John Adams expressed it well.

There is a voice within us, which seems to intimate that real merit should govern the world, and that men ought to be respected only in proportion to their talents, virtues and services… Few men will deny that there is a natural aristocracy of virtues and talents in every nation and every party, in every city and village”.

Jefferson’s agreement with this view is expressed in a letter to Adams from Monticello, dated October 28, 1813.

I agree with you that there is a natural aristocracy among men. The grounds of this are virtue and talents… The natural aristocracy I consider as the most precious gift of nature, for the instruction, the trusts and government of society. And indeed it would have been inconsistent in creation to have formed man for the social state, and not to have provided virtue and wisdom enough to manage the concerns of the society”.

The people of the United States of America, more than any other country I know, share the common attribute amongst many of it’s people of helpfulness. We Americans do help one another – it is one of our greatest strengths. It is easy to say that this attribute makes us happy but it is more than that, much more. It is part of the individuality of our nation that helping others – being useful to others – is something we do. It is one of the purposes of many of us: I claim it is the main purpose and it is a purpose that can bring happiness to both the giver and the receiver. Is this character trait disproportionately  linked to Americans?

Like Agassiz, in my own life I had no time to become wealthy but choose another route through life. I have helped others to become wealthy and some of those have found happiness, not so much in the accumulation of riches and power, but in providing help to others: their purpose of life became to be accountable, to be useful to humankind. Their life experience developed a personal morality that recognises the use they could be to society.


Comment: 01-dw

The issue produces many questions and, for me, no conclusions.

First, I suspect most people think that happiness is a state that is different than the dictionary definition. I think that we perceive happiness as a state of exhilaration which can be sustained for a long period of time.

If one were able to determine whether we should live a happy or useful life it still leaves the question: so what? And how do you measure such things. How do you determine if someone is happy. Do you go by their description and is that description for the moment, the past day or so, last week, last year? What is the period of time used for measuring happiness or, do you consider what you know or perceive of that person in addition to what they say to determine if they are happy? When you learned that your grand-daughter would live, was that happiness or extreme relief and great pleasure that all had worked out. How long must an emotion last for us to say it is how we are generally. What level of emotion must be attained before it can be declared the true emotion? Can you be happy yet vicious in your business practices. Is it legitimate if one is happy after repossessing their house from a family that could not afford the rent because they lost their job. Can one say they are happy yet be very dissatisfied with their partner or boss.

And what exactly does useful mean? Helping an old lady across the street? Fighting against the war? Fighting in the war? If fighting in the war is useful then does that mean that fighting against the war is not? Is one useful if they go to work each day but do nothing else toward the betterment of society?

Why must the debate be based on an either/or proposition? If I have felt happy at times but those times are insignificant in relation to the times I am content, discontented, angry, upset, depressed, fearful, uncertain or just neutral am I happy or something else?

Is it useful to give a penny to a homeless person seeking help or must one give a greater amount to be truly useful? And what if you give nothing in hope of forcing the government to recognise a serious social problem and do something about it? Is the latter a useful act though the beggar may suffer?

If we execute someone who has killed, is that a useful act or should we, as a society, have done something much earlier for that individual in hope of preventing such an act thereby being really useful?

And what combination of the two would be acceptable: 20% happy, 80% useful? fifty-fifty? and on and on and on.

What’s the purpose of the debate? To resolve a very difficult issue, to wonder about something that has no resolution or is it mental masturbation?

?Great questions and musings….  My own view of happiness on a yearly, monthly, daily basis is evolved greatly over my lifetime.  I used to think of happiness in dictionary terms (i.e, the joy of riding a roller coaster, the belly laughs between good friends over a drink), but now I have a much longer view.  I want to be happy.  Why not?  I choose to try to be happier over time.  I study what makes me happy and try to increase those activities and thoughts.  I see extreme happiness highs as rare, but delicious and I work toward achieving them over fairly long periods of time.  If I have an idea for something and work toward achieving it (mostly at work) I achieve some level of anticipatory happiness every day I feel I make progress toward that goal.  I become ‘in love’ with the idea.  The downside, is that if, on any given day there is either no progress or the dream is in jeopardy of dying, then I become more or less depressed.  This makes goal-setting sort of a high-stakes activity for me.  I set myself up for an extreme high or a bad fall.

I tell myself that I’m ‘saving up’ a series of highs that I can put in the proverbial memory bank so that over a lifetime I can feel the warm glow of those peak moments.

This is my simple plan…. Sometimes I think its working because I really do achieve many of my goals.  I may be deluding myself though because in the middle times between my highs I’m often not ‘living in the moment’.  Time is passing and I’m living in some future state of anticipation.  It doesn’t always work for me either.  I sometimes simply, intolerably and inexplicably lose my ‘spark’, my inspiration to achieve and I can go a few days trying to regain that ‘reason to strive’.  That’s when I usually tell myself I’m working too hard, begin looking for distractions, play more tennis, get together with friends, take long walks, etc.  But these episodes reinforce the ineffable mysteries of life and the perils of trying to live life on a plan (note my romantized explanation… very satisfying).

Comment: 02-fl

Mill’s “Utilitarianism” should be read e.g. “On the present occasion, I shall, without further discussion of the other theories, attempt to contribute something towards the understanding and appreciation of the Utilitarian or Happiness theory, and towards such proof as it is susceptible of those who know anything about the matter are aware that every writer, from Epicurus to Bentham, who maintained the theory of utility, meant by it, not something to be contra-distinguished from pleasure, but pleasure itself, together with exemption from pain”. When most philosophers talk about “happiness” what they really mean is something very like your definition- usefulness or utility. That doesn’t mean that we can’t have a good discussion about the topic. but we have to be exceedingly careful in the terms we use. We can’t casually say that happiness and usefulness are opposed. The more I think about it, the more I like using Mill as a touchstone: the big sticking point about utilitarianism, grossly stated as “the greatest good for the greatest number”, is why should you or I care more about the greatest good for the greatest number than we care about the greatest good for our family? Our greatest “happiness” comes from their good, not the world’s good. Right or not right? Mill’s utilitarianism is a good reading and can direct focus on some critical topics.

Comment: 03-am

I agree with your conclusions in the last two paragraphs.

Yes, helping others is a fine purpose for us. As you said, it brings happiness to both giver and receiver. But it conflicts with Ayn Rand’s tenet of pursuing one’s own rational self-interest. I’ve always had this problem with Objectivism. To me, the the whole ‘looking out for #1′ vibe taints the rest of Objectivism.

Mostly, her other observations make sense to me — reality exists separately from consciousness and our perceptions can lead to objective knowledge of reality via logic, blah blah. That’s all very Spockian (Mr., not Dr.), and appeals to my scientist core.

Comment 04 – ss

In what you have compiled already you do touch upon a very simple premise that comes from Jewish philosophy, which is that you will not find happiness in life unless you first find a way to be useful. Thus, in that sense, there is no debate to be had.  The purpose of life is to be useful but, by being useful, you will find happiness as a result.

Synthesizing life

Friday, May 21st, 2010

So what did The J. Craig Venter Institute do?

    Synthesized an exact replica of a string of DNA from Mycoplasma mycoides over 106 bases long and placed it within an empty cell membrane from a different species of the genus Mycoplasma [M. capricolum]. The cell functioned like a normal living organism. This is a significant achievement because long DNA molecules tend to break during manipulation. Previously a much smaller genome was built and implanted into a pre-existing cell membrane.

It has taken 10 years of Craig Venter’s effort to achieve this goal and it represents only a very small milestone in humankind’s future ability to create synthetic life. There are two main avenues to pursue from now on.

  1. Synthesized a cell membrane and cell contents, exclusive of the DNA polymer molecule, and repeat the experiment. This achievement will mean humankind can completely synthesize a living cell.

  2. Catalogue the DNA bases responsible for specific genetic traits in a specific species [this is currently an ongoing project at many research institute] and build an organism that has specific traits completely different from any other know form of life.

The aim is for scientists to be able to do these two activities routinely and at this stage humankind will have a marvellous control over prokaryotic living systems. Such knowledge will have vast potential for humanities colonization of our Solar System and beyond. I estimate it will take another 10 years to reach this goal.

Currently, science is taking a different approach to eukaryotic living systems. The approach is to catalogue the DNA bases responsible for specific genetic traits and alter a pre-existing germ cell [either the male or female gamete or both] to produce a zygote that is abnormal to the species in terms of its traits. This approach is moving along rapidly and has been achieved at a minor level e.g. photosynthetic hair. Success depends upon understanding [cataloguing] the base-pair to trait relationship in specific species; and, successfully inserting and/or removing base-pairs from gametes. The related investigation pertaining to somatic [body] cells also is progressing and can have far reaching effects on the health of individuals and the curing of disease.

The following is a direct link to the complete article published by Science magazine.

P-T-C adaptation and extinction: the case of the lizards.

Friday, May 14th, 2010

As a young scientist in the 1950′s I was introduced to thermodynamics by Turner and Verhoogen’s book [Igneous and Metamorphic Petrology1] which was the basis a course given at Sheffield University, England. I was intrigued by Bowen’s Reaction Series which related minerals to pressure-temperature and chemical environment, and how so many things in nature seemed to depend on one or more of these three variables.

At the same time I was deeply involved in palaeontology, palaeo-geography, human zoology and mathematics. As a student stratigrapher it was apparent that climate and the atmosphere were major controls on evolution. A course in mathematical climatology offered in the Geography Department integrated many of the ideas of thermodynamics into weather prediction and early forms of climate modelling – ideas that I was able to utilise in an expanding view of palaeo-geography as it extended through time as historical geology. These were all things that were bombarding my mind during my undergraduate years at Sheffield and it was not until later as I began reacting with P. C. Sylvester-Bradley on questions of the concept of a species and evolutionary theory that I understood the real importance of P-T-C in the history of life. Climate and the atmosphere played an immense role in the the development of Earth and it’s living systems: from the setting of the vast latitudinally controlled coniferous forests to the adaptation of the Tibetans to life in the Himalayas.

Articles like that of Dr. Barry Sinervo, professor of ecology and evolutionary biology at the University of California, Santa Cruz, on the widespread extinction of lizard populations as a result of climatic change are part of the continuous documentation of the importance of P-T-C on Earth’s development [Science, May 14th, 2010]. Accumulating an extensive database Dr. Sinervo’s group was able to document that extinction amongst lizard’s was due not to habitat loss but to climate warming [since 1975] that is driven by increased atmospheric CO2. The essential factor is well known to those who study the rattle-snake in that rattle-snakes use heat to warm up their body temperature but cannot stay in the heat too long – it will kill them. Rattle-snakes, once sufficiently warmed, move into the shade. It is the same with other amphibians and Dr. Sinervo notes that with lizards, once they retreat into the shade there is less food to hunt. The implication is that heat pushes the lizards into a cooling location and they die of starvation! “These lizards need to bask in the sun to warm up, but if it gets too hot they have to retreat into the shade, and then they can’t hunt for food. At the extinct sites in the Yucatan, we found that the hours per day they could be out foraging had collapsed. They would barely have been able to emerge to bask before having to retreat……We thought we’d see evolution occurring in response to climate change, but instead we’re seeing extinctions. Beyond a certain point, the lizards can’t adapt.

Science is definite in that factors other than temperature, pressure and chemical environment, come into play in the evolutionary process: catastrophic habitat loss for example. However, more and more research is showing the classical controls on adaptation, especially temperature and chemical environment, are major driving forces effecting Earth’s biocoenoses today AND these forces are a direct result of humankind’s activity.

1Igneous and Metamorphic Petrology,694 p., McGraw Hill, New York, 1951.

Archive for June, 2010

BILGE WATER: that big gas bubble under the Gulf of Mexico

Wednesday, June 30th, 2010

I did not want to get involved but now one of my children asked me questions so it is a different matter!

As some of you know I SHOULD understand what is going on.  I was director of Research for the Louisiana Geological Survey, helped organise the LGS response teams to the Exxon Valdez spill, was  Professor of Petroleum Geology at LSU, owned a company [Carbon System's] that specialized in locating methane gas bubbles prior to setting drilling rigs in the Gulf of Mexico, educated lawyers on the way oil and gas is generated, and generally studied the distribution of biogenic material on the floor of the Gulf of Mexico.

Firstly, there is NO huge gas bubble under the Gulf of Mexico that is ready to explode and cause a catastrophic Tsunami.
Secondly, oxygen depleted ‘dead zones’ exist at depth in all of the Oceans and the one’s in the GOM have been studied for a long time.
Thirdly, the clathrates containing methane in the GOM have the same origin as those existing at depth in all Oceans of our Earth and they are a water bottom phenomenon.
Fourthly, methane gas in petroleum reservoirs are mostly petrogenic methane formed by organic matter passing into and through the oil-window at depth.  This petrogenic methane is either dispersed in the inter-grain space in most sediments, or accumulate in traps where they form a top layer in the water-oil-gas accumulations in reservoirs.
Fifthly, biogenic gas, formed from bacterial degradation of organic matter at the surface and at SHALLOW depths, can form biogenic methane gas pockets of sufficient size to explode – but only if there is a sudden pressure release such as penetrated by shallow drilling when placing a drilling rig on the sea floor.  This is known to have cause destructive effects in the GOM in the past and is the reason why shallow drilling testing was/is done as part of the required hazard and environmental program prior to issuing a drilling permit by the State.

The Deepwater Horizon disaster is spewing out a lot of methane gas and this will have an adverse effect on the chemistry of the seawater and all life contained therein.  The bacteria in the seawater are more interested in the oil as a food source and hopefully will speed degradation of the hydrocarbons over time.  I certainly agree with Professor Kessler that there is a lot of methane being produced and it possibly is  ‘the most vigorous methane eruption in modern history’, however, it’s overall effect on Earth’s biocoenosis will be negligible.  It’s effect is felt primarily on people who are loosing wealth.  Because of the permanent ocean current-flow in the GOM those principally effected were predicted to be at the onset, and now are, the people of Mississippi, Alabama and north-western Florida, with minor effects on Louisiana.  If a hurricane hits coastal Louisiana that will change, especially in the brackish marshes which rely on daily tidal flushing for their vigour.

The following is un-scientific opinion.  Regarding the Federal Government policy of stopping all drilling I think the ruling was unwarranted – because the event was caused by human error.  The MMS was supposed to have had rules and regulations in place to fore-stall such an event as this Deepwater Horizon spill.  Clearly more is needed.  From the hundreds of eMails, interviews and discussions I have seen and read, those of ‘drillers’, and the few technicians on the Deepwater Horizon rig, seem to be the more knowledgeable.  It appears  that the disaster was caused by technical  people on the rig not reporting problems up through the system, those higher up in the system not understanding the potential disaster that could await; and, by some British Petroleum managers not being scientifically savvy enough and/or cautious enough.

Archive for July, 2010

Future technology for the taxonomist.

Sunday, July 4th, 2010

I have always been an admirer of IBM’s technology starting with using the old 360-370 machines and even on a rare occasion helping to repair a 370. IBM is one of the few corporations left that continues with the tradition that understanding basic scientific research is important  to the future of capitalistic endeavor.

Developing a tool that can provide accurate, fast and cheap DNA and RNA sequencing will be the principle break-though for biological taxonomy in the 21st century. I can imagine no other tool that will be of more importance to humankind’s immediate future in medicine, botany, zoology, sociology or any branch of life sciences. However, delivering a complete genome analysis for $100-$1,000 using nanopore technology, whilst a significant breakthrough, is not in itself the key. The key is to make nanopore DNA/RNA decoding units very cheaply! They need to be so cheap that every scientist that needs one can have one. They need to be as readily available as a good research microscope, and at base prices in the $1,000-$5,000 range with available software for data analysis similar to those currently found associated with scanning electron microscopes, X-ray machines and hydrocarbon well logging software.

Even in palaeobiology the study of fossil material can be advanced by such tools. I think there are places in the Devonian, Carboniferous and Permian where it is possible to find fossilized material in which the original organic material is not completely degraded to the level that all of the DNA has been destroyed. To sequence what remains of the DNA of such finds could lead to a huge understanding of past life.

The following video gives some background information:

See the Theoretical and Computational Biophysics Group research site:

gfh 04/06/2010

Archive for October, 2010

Pre-implementation genetic diagnosis

Saturday, October 2nd, 2010

Variants of the BRCA1 AND BRCA2 gene increase the risk of cancer and can be inherited from either the mother or the father. If you are a female and inherit the gene your risk of developing breast cancer or ovarian cancer is increase. The increase for breast cancer is dramatic with 60% of the women with the gene developing the disease in their lifetime. In males the possession of the gene increases moderately the chance of developing prostate and colon cancer.

To screen eggs, scientists take advantage of the body’s normal egg-making process. In the final step, the 23 pairs of chromosomes separate — one set goes to the nascent egg and the other set ends up in a tiny sac called the polar body. By comparing the DNA in the polar body and the woman’s DNA, scientists can deduce which versions of the BRCA genes are present in the egg.”  – The Los Angeles Times.

Pre-implementation genetic diagnosis can test for the presence of these genes in the female gamete and allow selection of good eggs to make a BRCA free zygote. The method allows the purification of the maternal blood-line and makes sound sense. There are other genetic traits that can use PGD and should be included in an analysis with the eventual goal of eliminating bad genes from as much of the human blood line as possible.

Currently, the technology is available to perform the necessary tests and select good female gametes. The medical procedures require specialized expertise and are expensive. Fundamentally the argument against application of the technique is entirely a moral issue and, thus, outside the bounds of science – as I have said before Science has ethics but does not have morals [Hart, 2008].

Government should sponsor improvement in Homo sapiens and do so by providing a federal, minimal profit, organization for pre-implementation genetic screening. Clearly, the sheer cost means that all women cannot be screened but for those that want screening a lottery system could be established. Those wanting testing but are unsuccessful in the lottery, if they have the wealth, can still utilize private enterprise clinics for testing: this is one of the strengths of the capitalist system.

All class [wealth] groups should be included in such a lottery because our system is based upon equality of access. I realize that arguments will be made that “those that can pay should pay” but this negates the concept of the New Global Society, one of the mandates of which is “equality of opportunity”. Moreover, it takes us down the slippery slope towards extreme Socialism.

In my eBook “Evolution and the future of humanity: Homo sapiens’ galactic future“, 2008. I discuss PGD under the section Eugenics.

Eugenics keeps on returning as an issue relating to social condition because repeatedly some people see the concept as not only logical but a clear way to improve the cultural gamodeme. Others cannot separate modern eugenics from the inhuman ideas of the last Millennium, and do not accept that germ line genetic engineering [GLGE] could improve the human condition. The past saw the use of numerous unsophisticated practices to ‘improve civilization’.    Marriage restriction, as in the apartheid era of South Africa; genocide, as practiced by Hitler; sterilization as a condition for legal abortion [as practiced by England during the latter part of the twentieth century]. These were all socially  visible methods that were eventually proven to be either illogical or impractical.”

Eugenics, when it is based upon GLGE, is a benefit to the social condition of humankind. The moral issues raised by many appear not only narrow-minded but also severely short sighted. I do not believe the rights of the unborn or un-conceived are related to moral issues. I believe morals apply to the living and the here-and-now. Indeed it is questionable whether or not we have a responsibility to our future phylogeny. We are the ones alive at this moment and we make daily decisions about what is best for us as individuals and for our own offspring. The sum total of these decisions is how the social condition changes. All human being’s have immense common sense when it comes to self-preservation and kinship, and most have an ability to assess information and make decisions for their own good and for the good of their kin. People take decisions that are both logical and desirable for their own and their offspring’s future every day. The process decouples us from the decisions our offspring might have preferred. Although such processes are conditional they are without feedback i.e. physical and cultural evolution is time constrained and the future cannot effect the past except as a thought experiment. This does not deny that future outcomes of present actions are conditional; or, that individuals and groups will continue to use speculation and predictive methodology about the future to determine their own future action.

Abortion is part of the eugenics issue. Prenatal testing, such as amniocentesis and chorionic villus sampling, provide information on the genetics of the fetus. This allows a decision to be made early in developmental stages regarding abortion. The possession of genetic diseases such as Down’s syndrome and Gaucher’s disease can be pre- determined this way. The choice to abort or not is an issue which religion attempts to interfere with greatly and is the cause of much antagonism towards religious groups. The abortion issue is being fought by one side under the banner of ‘freedom of the individual’ and especially women’s rights; and, on the other by laws said to have been given by a supernatural being. Linking the modern eugenics movement with the politically ill – conceived eugenics movements of the last century, in order to dupe those who are uninformed is equivalent to false advertising scams.

“Science is developing further ways to address the eugenics issue. For example, the abortion issue often can be avoided by pre-implantation genetic diagnosis [PGD]. The process takes place after in vitro fertilization and prior to implantation of the embryo into the uterus. A series of embryos may be developed in this way and they are examined in the Petri dish at the 8-cell division stage. One of the cells is removed from the embryo and subjected to DNA testing for known genetic diseases such as Tay-Sachs disease, cystic fibrosis and Gaucher’s disease. In this way, hopefully a disease – free embryo can be selected for implantation in the uterus. In the future, our phylogenic descendants may shift the entire process to an artificial womb. Many of these aspects of controlling population pressure are intertwined with genetic interventions on a more general scale.”


Wednesday, November 10th, 2010

by  George F. Hart Ph. D.

A recent post by Robert Lanza tweaked my interest [] primarily because it related to the last section of my eBook “Evolution and the future of humankind: Homo sapiens’ galactic future, and secondly because I think he has not got things quite sorted out yet!

He refers to some old ideas, reminiscent of Feynman's that history is determined by present knowledge, but relying on new experiments that “increasingly cast doubt on the existence of time as we know it.

I have often asked people the question: If I was standing in the doorway 3 seconds ago and I am now sitting on the chair - where is 'me standing in the doorway' now?' It is a question that rests on the idea that motion in space-time comprises an infinite number of time frames. I posed my 10 year old grand-daughter the question a couple of years ago and she had the insight to raise questions about the nature of reality.

Lanza appeals to biocentrism in which “space and time are forms of animal intuition. They’re tools of the mind and thus don’t exist as external objects independent of life. When we feel poignantly that time has elapsed, as when loved ones die, it constitutes the human perceptions of the passage and existence of time. Our babies turn into adults. We age. That, to us, is time. It belongs with us.” .

The confusion is that the evidence is that our Universe is constructed by the events in them, and this includes time. Time as a parameter of reality is thermodynamic time based on the 2nd law and it has a direction that is the same as psychological time. The idea that history is created by present knowledge andknowledge in our mind can determine how particles behavereally makes me pause and I do not believe it. We live and observe at a particular scale somewhere above the quantum and less than the multiverse and our cells cannot jump in and out of it. Unfortunately our mind - which is what we would like to move out upon death - is directly tied to our cellular structure. We are thus locked into reality i.e. the space-time within which we exist at any moment. Time is part of reality and not a human construct - so I disagree on that point. However, if we seek an immortality, that escapes psychological time, our only hope is that scientists can come up with a complete brain scanner in the next few years and trap each of our minds in a Cloud database for later activation! If you want to accept a belief system that purports that you can move out of this time frame, for example upon death, then become a fundamental Christian or Muslim or whatever. But that choice will be wrong. Hawkings explains the situation nicely: “However, there are at least three arrows of time that do distinguish the past from the future. They are the thermodynamic arrow, the direction of time in which disorder increases; the psychological arrow, the direction of time in which we remember the past and not the future; and the cosmological arrow, the direction of time in which the universe expands rather than contracts.[2009:194]

I think it MAY be possible to eventually download a complete mind as a digital entity and thus we should be able to exist and grow until the end of our Universe and maybe even beyond. I have written that our Universe may be an experiment of the creator[s]: whatever that is. If this is so then maybe we are the eyes, ears and other sensors of our part of our Universe and our knowledge is continuously being passed via another dimensional conduit back to that which created our Universe - so that the experiment we are in can be monitored. Our past would thus have some sort of existence beyond time. I like to believe that but my only evidence is philosophical hope! The fact that our Universe exists indicates that something must exist outside of our Universe! Hawkins and Mlodinow's 2010 comment that There is no way to remove the observer — us — from our perceptions of the world …is well known to be correct, as is the truism “perception is reality. However: “In classical physics, the past is assumed to exist as a definite series of events, but according to quantum physics, the past, like the future, is indefinite and exists only as a spectrum of possibilities.” has no proof in the reality at the scale humankind exists. It is the classical concept that both thermodynamic and psychological time follows not that of the quantum world. Because thermodynamic time is a parameter of reality we do not create it. Without consciousness, space and time would still exist: only psychological time would not! Einstein’s acknowledgement that “the distinction between past, present and future is only a stubbornly persistent illusionis a tribute to mathematical modeling of our Universe not to the existence of human consciousness.

Hart G. F. 2008. Evolution and the future of humankind: Homo sapiens’ galactic future. ISBN-13 978-0-9818642-0-4.

Hawkings S. 2009. The illustrated Brief History of Time. ISBN 978-0-307-29122-6.


Anything unobserved at the quantum level is just a probability, not an existence”  fl

Posted in Will the Universe be ours? | Comments Off

The Evangelical Lutheran stance on genetics

Thursday, November 25th, 2010

The recent draft report on the Evangelical Lutheran Church of America is a worth-while read.

The “Lutherans understand that the books of the Bible were written long before the beginnings of modern science and technology and before humans developed the power to directly alter the future of the planet through contemporary knowledge and technology. Scripture, for instance, never uses the word “genetics” and is not aware of its fundamental concepts .

The writers make a similar point I made in my eBook  [Hart, 2008] :

Christian participation in discussions concerning genetic knowledge and its potential benefits will be inaccurate and incomplete if we do not engage and learn from the humanities or from scientific and medical endeavors. At the same time, the meaning of genetic knowledge and the debates about its use will be inadequately explored and morally dangerous without attention to the wisdom of faith traditions.”

The Lutheran document addresses five areas of genetic technology:

  1. Genetic engineering in agriculture (biotechnology), including practices such as genetically engineering seeds or cloning plants and animals, and pharming.

  2. Molecular medicine, including practices involving stem cell research, genetic therapy, personal genomics and SNP mapping, as well as efforts to extend the longevity of human life to as much as three times today’s average.

  3. Procreative activities, including prenatal testing and screening, genetically aided assisted reproductive technologies (ART), per-implantation genetic diagnoses (PGD), and the artificial creation of new life forms (synthetic biology).

  4. Commercial delivery, including DNA testing for employment and health insurance, trade policies, patenting of genetic material and research processes.

  5. Social use or implications, such as in criminology and DNA evidence; potential implications include discrimination based on genetic profiling, the practice of eugenics and belief in genetic determinism.

The observation that many will not benefit from the fruits of genetic research is irrelevant in a temporal context. I have pointed out [Hart, 2008] that many social achievements start as social inequalities evolving by the powerful and wealthy taking initial advantage of developments but, in time, improvements trickle down to the people. Education and the right to vote are prime examples. I do not fear that the rich and powerful will be the only beneficiaries of genetic improvements: scientific developments intrinsically are socially neutral given sufficient time. Certainly, different nations will show different times for innovations to reach all people in any particular nation. However, change can only come from within and the Lutheran Church would be wrong to mandate global reach for genetic improvements: we are more of a global village today than ever before but must not directly impose our personal belief system upon other people and other nations. In asserting that “the greatest danger in genetic developments lies in the sinful exercise of radically extended human power and not in any specific scientific or technological development per se.” the writers of the document do set-up a scenario for intervention of their belief system into scientific advancement. “The temptation to misuse or abuse power always has been present in regard to human technology, but when human beings gain power over the genome in a global context, that temptation carries qualitatively new dangers. Exalted pride can be especially tempting because genetic knowledge allows humans to push against previous constraints and into ethically uncharted areas. ” Within my framework I believe this should read “morally uncharted areas” because I understand morals as a characteristic of a belief system but ethics as a set of rules whereby any group operates: moral values contain ethical principles but ethics does not have to be moral. The writers do get it right when they state:

As a community of moral deliberation, this church seeks to identify an ethical framework that will aid faithful deliberation and decision-making and undergird critical engagement and advocacy in the study and application of genetics.” Their purpose is a noble one which rests on the premise: “The human vocation in an age of unprecedented power is to respect and promote the community of life with justice and wisdom ”; and, “This church rejects the ‘technological imperative’, that is, it rejects the prevalent practice or belief that we are free to use any knowledge that becomes available to create any technological application if the market will support it. An economic approach that promotes the unfettered pursuit of self-interest carries little or no basic respect for the needs of participants in the community of life”. Certainly, decisions cannot simply be left to the mechanisms of the market.

In some areas a broader view was need. For example in rejecting human cloning they assert that “no individual should be brought into life for the sake of repeating another individual’s genotype”. I agree with this but in the broader context we will eventually send individual genomes, either frozen or as a replication formula, to other parts of our Galaxy and Universe in a robotically controlled space liner [see Hart, 2008]. This is a valid exception to any ban on individual human cloning.

That the “applications of genetic knowledge in any form must be evaluated by their contribution to a just society and care for the Earth” is again a point I agree with but “care for the Earth” can raise serious conflict. For example, I believe in Terra-forming our Earth: i.e. optimizing our planet, and indeed our Solar System, for human needs. A case in point is introducing into North America large African animals, such as the Elephant into Arizona and New Mexico, and, the Hippopotamus into the Atchafalaya Swamp; or, at a more local level importing exotic vegetation that is adaptable to local conditions but may well compete with the local biocoenosis: I would much rather have a genetically altered Siberian bush bearing edible fruit than my local Coloradan red-current, and believe the bears and other forages would adapt.

In asking the question: “whether genetically engineered food, and the practices associated with it, increase the availability and equitable distribution of food for people who are hungry in the short-term and increase the ability of people to feed themselves in the long-term.” the writers of the report show they are socially responsible in the broader context not simply from the viewpoint of their own belief system. They encourage Science by noting that the “church believes overly restrictive regulation must not be a default response to novel genetic technology. Regulation must be justified by specified concerns for the potential harm of a genetic application and its delivery or by the necessity to regulate toward equal access and use”.

A quite critical point made in the report is: “Social scientists argue that a balance of proprietary and public goods is necessary to enhance social welfare. It is significant, then, that the balance has slipped significantly so that genetic science and technological experimentation are increasingly carried out in private industry. It also is a worrisome trend when universities limit or withhold access to their work in hopes of the ‘possibility to patent’ and increased revenue streams.” The report “calls upon those in government and commerce to prioritize finding ways to direct the benefits of genetic knowledge and application equitably and with access for all members of the human family regardless of which segments of society a person can be identified with. It also encourages those in government and commerce to seek means to reestablish a balance between public and private research as the engines for genetic developments.” It is one tragedy of modern Universities that since the 1970′s they began turning themselves into businesses with Chancellors more interested in funding than good research, and with University Foundations devoting themselves less to funding faculty research than to generating wealth [the two do not necessary go hand-in-hand]. From a personal viewpoint I no longer advise a bright student to follow an academic career. One reason I left academics was because the administration look on the academic system as a business center, where pay-raises are given on how much funding an individual brought into the system – as said to me by a Dean.

As a scientist, a seeker of truth, and an atheist who believes our Universe was formed by ‘that which creates‘ I have always believed that religion has much too offer humankind, and often interprets well our humanity traits. The Lutheran Document is one I would recommend as a genuine attempt to approach the questions pertaining to the future of genetics in a ethical context. “Knowledge matters to moral insight. Those who possess expert knowledge relevant to decision-making have a moral duty to share what they know with others. It is part of their responsibility to enable participation of others in the process of moral discernment and policy adoption. At the same time, they must exercise appropriate humility about the range and durability of what they believe they know”.

The following, extensive quote, contains the significant points made by the writers of the draft of the Social Statement on Genetics by the Evangelical Lutheran Church.

The ELCA calls upon individuals, agencies, organizations, corporations and governments to pursue goals and to set policies that will:

Likewise, this church rejects goals and policies that will:

Likewise, the ELCA will raise vigorous questions about goals and policies that will:

Comment by Professor George F. Hart, 25th November, 2010.


Evolution as a collective phenomenon of Mathematics

Thursday, November 25th, 2010

A recent article in the Physics eJournal ArXiv caught my attention because it inadvertently highlights the fact that our K1-K12 science and mathematics education system is not good.

Nigel Goldenfield and Carl Woese [i] recently pointed out that evolution can be views as a phenomenon embedded in non-equilibrium statistical mechanics of a collective data-frame i.e. life is not chemistry it is mathematical physics. Many have recognized this basic premise for a long time, more so since the discovery of the DNA biological code, and have even attempted to apply the basic premise to understanding the evolution of human nature - including moral and ethical values. I am certainly one of those people but as I have said before: our understanding of mathematics is not yet good enough and we await a break-through in mathematical theory before we can thoroughly understand our Universe and life within it. Our Universe is a mechanical system and life itself is a biological machine originating as an emergent phenomenon from the complexity of physical systems and it's origin probably lies in the statistical interactions of crowd-like phenomena.

Goldenfield and Worse state: “if we are to understand our biology, we need a statistical mechanics of genes: the fundamental processes that have shaped us are strongly collective in nature, and need to be treated appropriately”, and, “it is timely to assess the extent to which a condensed matter physics perspective – with its underlying principles of collective behavior arising from interactions – can be illuminating in biology”. These statements in themselves are sufficient reason to read their article.

A phenomenon is understood if the reasons for the existence of the phenomenon are known, and, if we understand under “what circumstances a particular system … represents an instantiation or realization of the phenomenon”. It is not sufficient to know what is, we must also know what is allowable: and this presents a view that is greater than what we observe. Indeed we must break loose from the harness of perception is reality.

Elsewhere I have explained the three basic Laws that govern the evolution of life, and within Goldenfield and Woese's framework these are akin to a complex conditional, mathematical-statistical progression: “The fundamental evolutionary process within the cell was the extension of metabolic pathways, by modification NOT innovation. This indicates a uniformity of living systems going all the way back to the primordial cells i.e. it is a legacy system. The resultant cellular developments require neither a plan of some super-natural force, nor rational design. On the contrary they are the result of random thermal motion within water.” [Hart,2009].

Goldenfield and Woese's observation: “the majority of biologists would probably regard their primary role as being in one sense or another to reverse engineer the myriad specific realizations of organic life on Earth — the reductionist exercise that has been notably successful within its own terms of reference”, is generally true of neontologists but not so paleontologists. In paleobiology there is a basic realization that emergent phenomena underly evolutionary diversity, and any living system is in a constant state of non-equilibrium with its overall environment [The Law of Instability, Hart, 2009]. In such a system change has much to do with the statistical dynamics of the systematic.

It is unfortunate that Evolutionary Theory is still linked to the expression 'survival of the fittest' which is more of a media headline than a description of our modern concept of the evolutionary mechanism. That expression totally depends upon what one considers the word 'fittest' to mean: the concepts of emergence, complexity, and genetic novelty have been with us since, at least, the 1960's, and Professor Woese's 1971 [ii] publication on complexity was an important contribution to our understanding of nature. The problem has not been a recognition of a need for a more mathematical approach to either paleobiology or neobiology, but rather the lack of knowledge of how to correctly describe and analyze the living system in mathematical statistical terms. Goldenfield and Woese's article points out the problem rather than offering a solution to the evolutionary process. We need to set-out a more rigorous approach to understanding both life and our Universe.

A few biologists have began to explore mathematical procedures but the fundamental problem starts early and seems to lie at the level of our educational system - which tends to lack mathematical rigor. The typical 12th grade level of mathematics should be 10th grade if we are to improve our indigenous scientists ability to understand our Universe! Otherwise we will continue to import the above average IQ's from China, India etc., to fill places in our Universities. This is only a win-win situation if we can somehow send our lower IQ's to 'exotic places', never to return.

i Life is physics: evolution as a collective phenomenon far from equilibrium . ArXiv:1011.4125v1, 18th November, 2010.

ii C. Woese, “Evolution of macromolecular complexity,” Journal of Theoretical Biology, vol. 33, no. 1, pp. 29–34, 1971.


Comment by George F. Hart, 22nd November, 2010.