Can the Monist View Account for "What Is Life?"

self | February 27, 2005 | Alamo Girl and betty boop

[RightWhale]

The arrow of time is the object. The arrow of time does point both directions. While it is obvious that a broken egg won't spontaneously reassemble, other processes are happy either integrating or disintegrating. The arrow of time in the universe seems to point to increase of heat overall, while at the same time the universe expands even faster so there is an overall decrease of heat.

Perhaps a little geometrical picture will demonstrate. The arrow of time is running both directions all the time. We, living things, do indeed force the arrow to run in reverse within our regions of authority. We compose for a while and then we decompose. The arrow of time runs backwards while we live. Assuming life exists all aound the universe, it might be that this process will continue forever, and that it will eventually involve the entire universe if we can continue to grow into a Type 3 Civilization. We might already be a Type 3 Civilization but just a backwater outpost waiting to link up with the main effort. The arrow of time may already be running the opposite direction overall to what our little steam engine model indicates. There is nothing in the physical laws to contraindicate this.

[Right Wing Professor]

Then one of us is misunderstanding the argument, Professor.

I'm sure that is true, yes.

I am completely unpersuaded of the applicability of information theory of any kind to practical problems in biological chemistry. The existence of a couple of funded scientists who are trying to prove there is such a role is not persuasive. But in any case, you cannot treat the nearly identical behavior of nearly identical cells as separate bits of information. How intricate cellular communication is in a complex multicellular organism is an open question. But certainly, it is many, many orders of magnitude less complex than treating each reaction in each cell as independent. Such a calculation smacks of the familiar 'improbability of myoglobin' calculations presented on numerous creationist web sites, which persuade non-neophytes of nothing except the author's naivety about probability calculations.

Are you (implicitly) suggesting that a person who thinks there are very good reasons why biology may well be irreducible to physics is expressing a “religious” view?

I'm saying that the people I know who do so are generally motivated by religion, and not by scientific evidence. (And also, if you want to avoid confusion with a YEC, stay away from the standard YEC bag of tricks:-)).

My opinion on the physicalist/non-physicalist debate is that it's premature; we know of no non-chaotic system that does not display determinist dynamics, and a philosophical distaste for determinism is not sufficient scientific grounds for rejecting the premise that biological systems are determinate. Moreover, we know enough of very simple living systems to expect that if they were not deterministic, we would have seen evidence of non-determinism. For example, we have mapped out not just the genome, but also the proteome , of some bacteria. If we know every gene; if we know every protein and RNA gene product; if we've determine all their 3D structures (and we're getting there); if we know their functions, and how they interact (ditto); and we have no evidence of any special fields or forces or anything that indicates that they behave other than by the evolution of physical/chemical laws; then I would say that we're in a pretty good position to discount vitalism at the level of a single cell.

But more importantly, I would say that you and AG are playing the age-old game of God-in-the-gaps. You're positing new entities, not because of a manifest inadequacy in established ones, but because you badly want those entities to exist, and you can identify niches where current experiment can't disprove them. That surely isn't scientific.

[furball4paws]

If I remember correctly, it was Feynman that said that a positron was nothing more than an electron going backwards in time.

Anybody else misremember this like I don't?

[bvw]

Okay, what stops G-d from acting in the gaps? An honest admission that there are gaps, that is too.

A hallmark of a good human designer of any sort is how smooth the design is -- say a design of clothing that fits, performs and styles so well it feels like an "organic" part of one's body. Why deny that possible aspect to all creation?

Such denial is a "Disney-esque" belief system ---meaning like a child's who visits the make-believe land of Disneyland or Disneyworld, accepting -- demanding -- that the make-believe is as fully real as are his parents. The folks at Disney -- the engineers, the designers, the technicians, the actors, the staff -- are each and every one keyed to maintaining that pleasant and joyfull delusion. Yet at Disney's palaces and playgrounds -- all is unreal!

[Cvengr]

You're positing new entities, not because of a manifest inadequacy in established ones, but because you badly want those entities to exist, and you can identify niches where current experiment can't disprove them. That surely isn't scientific.

You miss the point. Here is a little clue, (no sarcasm implied)....consider that gnostics and magi placed considerable import on the element of thinking.

Scriptural references to Egyptian courtisans casting their walking sticks on the ground and they became serpants, but they still were no match for the stick cast on the ground by a man of God, which snake consumed the others.

Consider Christ walking on water and Peter also for a bit.

Some allude that it is possible for faith to effect the physical world and not merely by influencing the soul, but by impact upon the physical.

Consider the nature of science. It first presumes a hypothesis, then tests it. If the gnostic had part of the story correct, physics in some part is influenced by thought. Just because many laws of physics do not allow some experiments to fruitfully acknowledge some aspects of hypothesis doensn't exclude the possibility that the thoughts of others haven't righteously prevailed.

BTW the gnostic view in incorrect, but not because of the attention to the craft, but because of its failure to abide by the will of God. This doesn't cast out all scientific work, rather it recognizes the scientific method, in and of itself, might beg the question of faith.

[bvw]

Parts of what is called evolution are factual. In whole? No. At best a working theory that has demonstrated usefulness in organizing data, but it lacks in many areas too. Statistics -- probability -- is one major one!

I'll join to Lord Kelvin in that -- let Steven J Gould show the probabilies vetted through harsh peer review. He can't right now -- even if he had them -- because the very peer review process is hopelessly biased at this point. One can only be harsh against any doubter of the grand castles and towers.

[longshadow]

symmetry placemarker

[freedumb2003]

When it's not dormant, what is it doing, do you think?

DNA at play between dormant periods

[ckilmer]

Public release date: 28-Feb-2005

http://www.eurekalert.org/bysubject/chemistry.php Contact: Octavi López Coronado
octavi.lopez@uab.es
34-93-581-3301
Universitat Autonoma de Barcelona

UAB scientists discover the origin of a mysterious physical force Discovery will led to improvements in the chemical, pharmaceutical and food industry



Ever since the 1970s, scientists have been trying to establish the cause of a repulsive force occurring between different electrostatically charged molecules, such as DNA and other biomolecules, when they are very close to each other in aqueous media. This force became know as hydration force.

Jordi Faraudo, a researcher for the Department of Physics at the Universitat Autònoma de Barcelona, and Fernando Bresme of the Department of Chemistry at Imperial College London have studied this mysterious force in detail and have discovered where its origins lie.

In the same way that a flag flutters in the direction the wind is blowing, at a microscopic level water molecules are gently attracted towards the direction in which an electric field is pointing. However, when the water is in contact with surfaces that create small electric fields, such as chemical compounds like those found in many detergents, this is no longer the case: the water molecules have a remarkable capacity to organise themselves into complex structures that are strongly orientated in such a way as to cancel out the electric field, and on some occasions, to reverse it. This abnormal behaviour was discovered by the same researchers and published in Physical Review Letters in April 2004.

The scientists have now discovered that this strange property is responsible for the hydration force that acts when water is surrounded by certain types of electrostatically charged molecules, such as DNA and some biological compounds, and when thin films form in detergents. The discovery has been published in today's edition of Physical Review Letters.

Water is the solvent in which most physical, chemical and biological processes take place. Therefore, it is essential to understand the nature of interactions between molecules dissolved in water in order to understand many of these processes. Two of the most important of these processes are the adherence of substances to cell membranes and the withdrawal of proteins. Both of these are fundamental in biomedical research, since a substantial part of the process of designing new drugs is based on understanding how substances penetrate cell membranes to enter cells. These drugs are often proteins designed to prevent or strengthen the action of other substances. In these cases, accurately identifying the protein folding is essential, since the form these proteins take on when they fold influences how effectively they are able to act.

Fully understanding the properties of this force that occurs when molecules surrounded by water adhere to each other is also useful in the chemical industry, particularly when involving mechanisms in which colloidal suspensions must be stabilised, such as the mechanisms used to produce paints, cosmetics and food products such as yoghurt and mayonnaise.

###

[shubi]

"No. At best a working theory "

There is no such thing as a "working theory". I am not going to tell you what the truth is, because I think you are being purposely deceptive. You have been on these threads too long to be that uninformed about how science works.

[longshadow]

re: Arrow of time

http://info.web.cern.ch/Press/PressReleases/Releases1998/PR06.98ETime_27sarrow.html

[Ichneumon]

Moreover, we know enough of very simple living systems to expect that if they were not deterministic, we would have seen evidence of non-determinism. For example, we have mapped out not just the genome, but also the proteome , of some bacteria. If we know every gene; if we know every protein and RNA gene product; if we've determine all their 3D structures (and we're getting there); if we know their functions, and how they interact (ditto); and we have no evidence of any special fields or forces or anything that indicates that they behave other than by the evolution of physical/chemical laws; then I would say that we're in a pretty good position to discount vitalism at the level of a single cell.

I'd like to second that argument. Well said. The same argument also applies to attempts to invoke a "will field" (or whatever) hypothesis which incorporates even the survival mechanisms of single cells, since again the processes by which these mechanisms operate are (in most cases) well understood, and act in "mechanical" fashion by the ordinary rules of chemistry and so on.

Also, much more is already known of some bacteria than just the genome and proteome. For example, complete biochemical pathways are now known for most of the activities which take place within E. Coli bacteria. See for example:

Global Properties of the Metabolic Map of Escherichia coli

Abstract: The EcoCyc database characterizes the known network of Escherichia coli small-molecule metabolism. Here we present a computational analysis of the global properties of that network, which consists of 744 reactions that are catalyzed by 607 enzymes. The reactions are organized into 131 pathways. Of the metabolic enzymes, 100 are multifunctional, and 68 of the reactions are catalyzed by >1 enzyme. The network contains 791 chemical substrates.

Functional Versatility and Molecular Diversity of the Metabolic Map of Escherichia coli

The Escherichia coli MG1655 in silico metabolic genotype: Its definition, characteristics, and capabilities

Abstract: The Escherichia coli MG1655 genome has been completely sequenced. The annotated sequence, biochemical information, and other information were used to reconstruct the E. coli metabolic map. The stoichiometric coefficients for each metabolic enzyme in the E. coli metabolic map were assembled to construct a genomespecific stoichiometric matrix. The E. coli stoichiometric matrix was used to define the system’s characteristics and the capabilities of E. coli metabolism. The effects of gene deletions in the central metabolic pathways on the ability of the in silico metabolic network to support growth were assessed, and the in silico predictions were compared with experimental observations. It was shown that based on stoichiometric and capacity constraints the in silico analysis was able to qualitatively predict the growth potential of mutant strains in 86% of the cases examined. Herein, it is demonstrated that the synthesis of in silico metabolic genotypes based on genomic, biochemical, and strain-specific information is possible, and that systems analysis methods are available to analyze and interpret the metabolic phenotype.

(Loose translation of the above: The E. Coli proteome and its expected protein and metabolic chain interactions can be "run" as a computer model (based on what is known of the way in which proteins interact), and already the model is at least 86% accurate in describing the actual biochemical reaction chains in living E. Coli and exactly how the bacteria will respond when various genes are deleted. This provides excellent support for RWP's point.)

There is an excellent overview of the metabolic map of E. Coli here. It includes the same image as the following, but in a form clickable on any node or pathway in order to view detailed information about the selected pathway, involved genes, regulation schematics, and more:

And this site has E. Coli metabolic maps displayed more in "poster form", for example (low-res form):

[Ichneumon]

let Steven J Gould show the probabilies vetted through harsh peer review. He can't right now -- even if he had them -- because

...because he's dead.

[onedoug]

By all means, Thank You.

Psalms 19:1-3 is said in the Saturday synagogue service. So cool....

Everything good.

[js1138]

dead placemarker

[bvw]

Another reason. Yet if a man's work is worthwhile it lives on in his students and associates. So they could.

(Also might you please not < img src > to huge files (huge being over 500 kb or so. They drive my browser on my other machine batty.

[MHGinTN]

Most enlightening. Thanks for the ping!

[bvw]

Second paragraph in that linked "arrow of time" CERN piece begins thusly:

The reason why the future and the past are so different in our daily lives is because the Universe started off in the Big Bang in a smooth and organized state. However, as the Universe expanded it became more irregular and disorganized.

IIRC, that's no longer considerd the case. Keystone removed, arch falls.

Minkowski -- HE understood time. the rest are lollygaggers.

[bvw]

My degree is in Physics. Yours theology? There are working theories.

I worked with a swiss-german once -- he could not comprehend anything unless it was in a laplace transform. Things can be expressed a zillion ways -- each valid -- but his mind was so set in its way, the method of expression has to be "Just so."

The fusterer, the dilletante, the idiot-savant, the arrogant bully of the intellectual workplace are all known to follishly insist on misapplication of precision. Of demanding more than needed or respectable. Giants such as Aristotle and Solomon -- and further back than they -- all recognized that in each endeavor, business, expression there is an appropriate measure.

[Doctor Stochastic]

The laws of both classical (Newtonian) physics and quantum mechanics are time-reversible.