Thursday, December 30, 2010

Are spirits only for drinking?

Isn't amazing that so much of Western religion depends on a single assumption: the existence of a soul or spirit.

Now, what do I mean by a soul? From an Abrahamic point of view, the soul is that immaterial entity that is supposed to be 'sitting' behind our eyes, driving our actions. This spirit interacts with our bodies and minds, and most remarkably, existed before birth and survives our death.

With these traits, the spirit must be physical in some manner and in principle, measurable. At what level does the soul interact with the brain? Does it interact at the sodium ion level in the neurons that are part of the neural signal process? Does it interact at the cell level? Or is it at the whole brain level? What is the mechanism? Or is the soul just the mind? The complex patterns of neurochemical signals make up the mind and in some sense, the mind is like computer software. If that's the case, the mechanisms of interaction can be found and are the subject of active neuroscience research.

But that mind depends on the physical properties of the brain. And without that brain, the mind has no place to run (at least until technology makes that possible). How can that survive death without some 'upload' process? And since that mind is information, a complex pattern, that depends on physical processes, how can that pattern exist without some physical container? Any entity that is not material, that is not measurable in any way, does not exist in our physical reality, and is in fact, immaterial.

So, does the soul exist? I think yes, if all that is meant is the mind; a mind that develops and grows through life, but disappears and disintegrates upon death. But if the soul is some ethereal entity that has no physical form or is not measurable, then I don't think that such a soul exists. And without an eternal soul, what meaning does religious salvation have? The threat of hell or the promise of paradise, which many contend are the hallmarks of Western Abrahamic religion, ends up being meaningless.

Wednesday, December 29, 2010

The MikeM Manifesto

As may be gathered by reading some of my other posts, I do have a few biases, which I will spell out. The first is that everything existing in the natural world can be explained by natural processes only. The second bias is derived from the first, and that is that anything outside of the natural world can not interact with the natural world unless it's through natural processes. The third bias is that the only way to know truth is via the scientific method. And the fourth bias, is that truth is approached asymptotically: certainty is impossible.

What do I mean by the natural world? I equate it with physical reality defined by the 4 dimensional space-time that we humans experience in our lives. This leaves open the possibility of extra-dimensional entities interacting with our reality, although such interactions can only occur via the four primary physical forces. All natural processes are measurable in principle, although in practice, our technology may not be adequate to resolve all the details of these processes. Without modern technology, it would not be possible to measure or manipulate electric or magnetic fields, yet they have always been measurable in principle. Physical or Natural Laws are the interactions of these natural processes with physical reality, so as such it makes no sense to state that natural laws can be suspended. In the case that a physical law appears to have been suspended or 'violated', it would be more proper to state that we do not have all the details of the case in question and have not grasped the limitations of our understanding of the physical interactions.

An example of this would be the change in behavior of objects at extremely high velocities. The laws of physics appears to be violated. But this appeared as such because our understanding of the relationship of objects with velocity was not adequate with Newtonian physics. Newtonian physics is what drops out, when the limit of the ratio of an object's velocity to the speed of light approaches zero. Special relativity becomes Newtonian physics at low velocities. Newtonian Physics has been used for the majority of the planet's civil and mechanical engineering projects and we have landed humans on the Moon and rovers on Mars using it. It is not complete, but we have a better understanding of its limitations for velocity. (and size, gravitational fields)

I admit that the statement "the only way to know truth is via the scientific method" seems absolute, but given the other options, I can't see any alternative, valid statement. There are 4 methods of knowing, or as Charles S Peirce puts it, "Fixating Beliefs": Tenacity, Authority, Reason, and Science. I will briefly go over each, although Peirce did a much better job in his essay, "The Fixation of Belief", .

The first method of knowing is Tenacity or the method of personal revelation. This method reduces down to a person fixating on a belief solely due to personal revelation (ideas which came to her out of the blue) and stubbornly holding on to that belief despite anything, usually evidence to the contrary.

The method of Authority depends on the supposed superiority of an outside agent to determine or settle truth. The agent can take the form of a person or meme. It depends on the ability of the authority to overcome disagreements as long as those subject to the authority remain subjected. The Bible and Qur'an are examples of agents of Authority.

The method of Reason relies solely on "what is agreeable to reason". This is an intellectual method, but is subject to whims of modes of thinking and paradigms. It can be logically based but not linked to evidence.

Lastly, there is Science. This method depends on empirical measurements, self testing, criticism and continuous improvement. Science is an algorithm, a process of learning that methodically approaches truth, and as such, it may never reach Truth.

So does this rule out a 'supernatural'? That depends on what is meant by the 'supernatural' If, as most claim, the supernatural is 'beyond nature' and not subject to natural laws, then I would submit whether or not a supernatural exists is immaterial. Anything that is claimed too be supernatural is beyond our knowledge or capability to know. All claims of a supernatural interacting with our world are therefore automatically suspect, and in fact, make no sense. Any claim of knowing the supernatural is also suspect. At best, those entities that appear at first glance to be supernatural are indeed natural: we just do not have the understanding of the physical processes. Isaac Asimov once said that a sufficiently advanced technology would be indistinguishable from magic.

TO BE CONTINUED (amended, edited, etc.)

Peirce, C.S. (1877), "The Fixation of Belief", Popular Science Monthly, vol. 12, pp. 1-15.
Charles S. Peirce, Selected Writings

Wikipedia Entry

Tuesday, December 28, 2010


I have been spending an obscene amount of time chatting on Yahoo chat in the Christian chatrooms (CC9 to be exact).  Why is that?  It's not because of my religion, since I have none.  It seems that I like the conflict with the crack pot believers.  I also enjoy reading their take on religious belief, current issues and events.  I've saved umpteen hours of conversations and planned on editing that into a compilation of whacky ideas and beliefs.  For the more sensitive out there, these chat rooms aren't populated by your typical, run of the mill believer.   These true believers are impervious to evidence or contrary ideas, and most display their total ignorance of basic science, philosophy and history proudly.  They proudly hit the ignore button on anyone who contradicts them, and strangely enough, broadcasts that action to everyone in the chatroom.  It is something to be experienced.

Alas, despite my enjoyment, I must cut back on the time I spend in there.  I'm not saying anything that makes a difference, and the other non-believers that I've gotten to know in the room, are only there fleetingly.  The rooms also give a strong illusion of friendship and of knowing people, strictly from their thoughts typed onto the screen.  I find that I lose interest in being in the rooms unless my 'friends' are there.  This just tells me that I need to connect with my friends and make new friends, IN REAL LIFE.

So to my chatroom buddies that may be reading this, so long.  I may be popping in here and there, just to whet my appetite, but I will endeavor to spend less time in the rooms.  I am hardly perfect and I expect that I will break and join in.  If I do, please remind me of this note and post.

Monday, December 27, 2010

Ethics of Scientific Research - Final Exam Question 2

This was my answer to question #2 of the Ethics of Scientific Research Philosophy Class from Autumn Quarter 2009

What is the role of competition in scientific research? How does competition help research? How does competition hinder research? Discuss the effects of competition on the Human Genome Project and/or the events surrounding Rosalind Franklin and Photo 51.

Competition’s role in scientific research was clearly demonstrated in the Human Genome Project. In fact, many of the last century’s technological and scientific triumphs, from the development of nuclear energy (and weapons), the technological development of high speed, commercial air travel, the development of manned space flight leading to the landing on the moon by humans, and to the development of the personal computer, were positively driven by competition. Competition is a fact of life due to the limitation of resources and due to the human desire for recognition. Competition ultimately helps scientific research; however, competition also exposes the dark nature of humanity and in some instances actually hinders scientific research.

Resources are scarce. This single fact drives a race to gain a portion of those resources for one’s own use. This race, this competition, motivates individuals to work faster, to conserve resources and prevent waste. Competition drives individuals to form coalitions, to pool resources and efforts , to gather the best minds together to solve problems. Competition inspires dedication, innovation and the search for better ideas. The role of competition in scientific research is encompassed by the entire aforementioned elements. The nature of the competition could be between academic groups, between commercial groups, between public and private groups or between governments and/or nation states.

On large scale efforts that take man-years to finish can be accomplished quicker with pooled resources and efforts spurred by competition. Even on small scale projects, innovation and new ideas are spurred by competition. During the Second World War, the fatal competition between the Allies and Axis powers led to a perceived race to the development of the atomic bomb by the Manhattan Project. In a few short years, the dedication and innovation of the researchers led to advances in the knowledge of nuclear devices and in the subsidiary technologies involved in deploying those weapons. Regardless of the morality of nuclear weapons, the research involved was positively helped by the perceived competition. The less fatal competition between the Soviet Union and the United States led to the development of heavy launch vehicles that sent humans to outer space and to the surface of the moon. Those also led to the fantastic journeys of unmanned robotic probes to all of the planets of our solar system, all within 40 years of the first flight into orbit. Competition in this case was also positively helped by the competition.

Science is hindered by the breakdown of trust, by lack of communication, and by neglecting moral obligations. The ugly side of human nature is exposed in some competitions, and can hinder scientific research. The race to be first may tempt some to falsify data, steal data, plagiarize results, and to perpetuate outright fraud. This leads to the breakdown of trust necessary to the exchange and use of ideas in science. It also leads to problems with public acceptance and support of research. One case in point is the outright fraud surrounding Piltdown man. Despite the exposure of the fraud by scientific researchers employing better scientific techniques, the fraud instilled a distrust of evolutionary biology in the less educated segments of the general public that persists to this day.

Competition may lead some to withhold data and block the free flow of ideas. Science depends on the honest and free flow of information between investigators through both informal means and through peer reviewed publications. Competition may also tempt some to violate moral principles, such as the principle of inherent human dignity and worth, non-malfeasance, autonomy, beneficence and justice. The temptation to use people as mere means to an end may also be manifested. These failures of moral obligations also hinder scientific research through the breakdown of trust between researchers and between researchers and the public.

The Human Genome Project demonstrates many of the positive aspects of competition helping scientific research. The entrance of Craig Venter into the race to sequence the human genome spurred technological advances and innovation that ultimately led to the entire project being completed under budget and ahead of schedule. The rapid dissemination of ideas and data on the public portion of the project helped other members of the public portion as well as the private portion. Many public institutions got involved to ‘beat’ the private venture led by Venter. Advances in computer analysis and automation driven by Venter’s ideas and public institutional spending sped the completion of the project. Venter’s motivation was primarily commercial in nature, evidenced by his lucrative lifestyle and interests, but there also appears to be an element of pure scientific motives. As such, there was some hoarding of data to protect Venter’s company’s interests, but overall the competition helped this research project.

The discovery of the structure of DNA, while publicly attributed to Watson and Crick, is surrounded by events that serve as an example of the negative aspects of scientific competition. Rosalind Franklin’s work in crystallography and the images she took of DNA were essential in the discovery of its double helix nature. She had provided critical reviews of previous attempts to determine the structure of DNA and was a leader in the field of molecular structure determination. However, the conflict of interests of her supervisors and peers led to the outright plagiarism and theft of her work.

Her peers, Maurice Wilkin being one, were involved in the suspicious transfer of the critical DNA image, Photo 51, to Watson and Crick without her approval or knowledge. Wilkins appeared to have several conflicts of interest in his dealings with Ms. Franklin, one of which was that he was a personal friend of Dr. Crick. Her supervisor, the head of her department at Kings College in London, colluded with the head of Watson and Crick’s lab to ensure a favorable publication in Nature for Watson, Crick and Wilkins. In essence, Rosalind Franklin was used as a mere means to an end, a violation of a basic moral principle.

Competition hindered scientific research in this case due to moral failings of the principals involved. Even though in the end, the structure of DNA was discovered by these efforts, research may have proceeded at a better pace if all of the participants were aware that they were involved in a competition. Rosalind Franklin appears to not have been aware of the competition. If she had been asked to collaborate, she may not have concentrated on the ‘A’ form of DNA, while only giving a cursory effort on the ‘B’ form that ultimately provided the key clues to the molecular structure of DNA. She could have advanced the research by several months if not years if she had been more fully involved. In the end, her significant and vital contributions were ignored and forgotten by the public at large.

Competition is a prime driver of human innovation made necessary by the limitation of resources. And even though competition may expose the dark nature of humanity and tempt many into failing their moral obligations, it is extremely helpful in scientific research, and in general it helps more than it hinders.

Ethics of Scientific Research - Final Exam Question 1

This was my answer to question #1 of the Ethics of Scientific Research Philosophy Class from Autumn Quarter 2009
From the researcher’s perspective, is gene patenting a good thing? Articulate your stance on gene patenting and justify your thesis using either Kantian theory or utilitarianism. Discuss and respond to one possible objection to your argument.

The Human Genome Project advanced the technology involved in exploring the genetic code found within the human cell as well as all living beings. Gene patenting, a serious legal and ethical issue, arose from this advance in science and technology. Attitudes regarding the patenting of genes vary among the stakeholders, but from the researcher’s perspective, gene patenting is not a good thing. The ethical nature of gene patenting, however, is ultimately not subject to the perception of the stakeholders. The patenting of genes is not an ethically sound use of intellectual property laws and Kantian ethical theory supports this stance.

A gene is the sequence of nucleic bases, adenine, guanine, thymine and cytosine (A, G, T, C) present in DNA that ultimately produces, via mRNA transcription, ribosome mRNA translation and tRNA assembly, a protein in a cell of a living entity. The technology and science of gene sequencing involves the extraction of DNA from an individual living being and the determination of the sequence of the nucleic bases in that DNA. Defining the particular sequences of nucleic bases that constitutes a gene involves determining what chromosome contains the gene, what portion of that chromosome contains the gene, and determining what protein the gene encodes. The genes and chromosomes are inherent in the total genome of an individual, whether that individual is a bacterium, a plant, or an animal, including humans. Human ingenuity is involved in these discoveries; however, the particular DNA sequence that defines a gene and the protein that it encodes was present within the population long before the advent of gene sequencing.
Patents are intellectual property rights conferred upon an inventor or assignees for a limited amount of time, usually 20 years from the time of filing an application for the patent. A patent guarantees exclusive rights to an inventor to prevent others from using the invention without the inventor’s permission. However, academic researchers have an exemption that allows for the production or use of the invention for research use only, without the permission of the patent holder.

Patents are awarded for an invention based on the following considerations: it is a product of human ingenuity, its novelty, its non-obviousness, its usefulness, and its reduction to practice. Prior to the Supreme Court of the United States’ ruling in Diamond v. Chakrabarty in 1980, living things were held to be unpatentable, since they appeared to fail the aforementioned considerations. However, that ruling changed the allowable items that can be patented to include living beings.

Diamond v. Chakrabarty (1980) involved the patenting of a genetically modified bacterium to clean up oil spills. The ruling, which awarded a patent to Dr Chakrabarty, set the legal precedence for all the subsequent biotechnology patents including genetic patents. The legal leap from a human defined, genetically modified bacterium, which in many ways has the characteristics of being a product of human ingenuity, to the patenting of portions of the genetic code inherent in all living beings, exposed several ethical issues. The legal details of the leap are not relevant to the ethical issues at hand, and will not be discussed further.

A patent on a gene guarantees the exclusive rights to the use of the genetic information and its associated protein. These rights confer on the researcher or assignee a monopoly on the gene and protein that may be present in all living organisms due to the genetic interconnectivity of all life on Earth. When applied to genes found in the human genome, this property right, to a part of all of our bodies, is conferred to a limited group of people. This essentially treats living beings and people as no more than assemblages of commercial products. This is the core of the ethical issue at hand.

In Kantian ethical theory, the respect of humanity version of the Categorical Imperative (CI) states that one should treat humanity always as an end in itself, never only as a means. Human beings have intrinsic moral dignity or worth, we should not abuse, manipulate, exploit, or deceive people in order to achieve specific goals. The universality version of the CI, that people should act in such a way that one's conduct could become a universal law for all people, is also relevant to this discussion. The concept and practice of gene patenting violates the ethical principle that human beings have intrinsic moral dignity or worth. A property right to parts of a body is different only in scale to a property right to the entire body. Property rights to an individual are a denial of the intrinsic moral worth of the individual. This violation of such an important ethical principle is not a practice that should become a universal law for all people, and therefore, the patenting of genes is not an ethically sound use of intellectual property laws.

Academic researchers are motivated by the “Publish or Perish” nature of academia and have a desire to monopolize information prior to publication. Tenure, promotions, further grants, and possibly reduction in teaching duties are rewards for being the first to publish and significantly contribute to a field. Ideally, academic researchers have no interest in patent protection, while their academic employers, while interested in institutional reputation, may be interested in the financial gain from the monopolization of intellectual property. Non-academic researchers while still motivated by the pure science involved are ultimately motivated by the financial rewards associated with success as well as the financial reward of continual employment. Their employers are interested in the return on the investment made and often insist on the complete ownership of all intellectual property created by the employees.

At first glance, the commercial operation and researcher have a vested interest in monopolizing the fruits of their efforts via patent protection. But researchers should be wary of this approach. Applying the universality version of the CI, they should act such that their behavior should become a universal law but the universality of such behavior would severely hinder further research. Due to the nature of the US Patent system, applications for a patent are not public knowledge, and research into a gene could be unwitting patent infringement. Fear of litigation being such a strong deterrent to action, research would grind to a halt. Hence, one of the prime arguments for gene patenting, that it promotes competition, is compromised by the squelching of all research.

The protections offered by a patent on a gene may provide a motivation to finish first and to beat the competition. Without that protection of the intellectual property rights, the desire to invest resources to an endeavor that would not have guaranteed returns due to monopolization would not be present. The consequences from not competing could be waste of resources and even the avoidance of research. However, Kantian ethical theory is not concerned with consequences; it is concerned with the duty of moral agents to act morally. If all researchers patented a portion of the genome, then individual humans would in essence be parceled out into a mosaic of intellectual properties. Human beings have an intrinsic moral worth and gene patenting is a clear violation of that ethical principle.

Testing, Testing ... 1, 2, 3

To all my countless fans out there (countless since you can't really count zero), I have not given up the blog. Well, not yet.

But, as a test of the Emergency Time Cube alert, I will do the unspeakable. I will mention the name of

David Mabus  aka  Dennis Markuze

and see if what is said is true.