Comments.
From your link:
http://star.tau.ac.il/~inon/wisdom1/preprint.htmlBacterial Wisdom, Gdel's Theorem and Creative Genomic WebsEshel Ben--Jacob
School of Physics and Astronomy
Raymond & Beverly Sackler Faculty of Exact Sciences
Tel-Aviv University, Tel-Aviv 69978, ISRAEL
{note - I have deleted most references and many parts inside paragraphs to make this as brief as possible}
Introduction:
Eshel Ben-Jacob writes:
The power of the Darwinian picture lies not only in its achievements, but also in the dismay evoked by what seems to be the only alternative - Vitalism ...
... erm, ... the "only alternative" ... ? Can anyone spell "strawman argument" eh? Had to look up "Vitalism" as it is sooo popular now:
Vitalism - Wikipedia and
vitalism - The Skeptic's Dictionary - Skepdic.com. Looks like ID type "there's just
got to be more to it" thinking, so I guess that fits here.
My basic assumption is that the observed creativity in nature is not an illusion but part of an objective reality, and as such should be included in our scientific description of reality. ... After all, creation means emergence of something new and unpredictable, something not directly derivable from the present. ... My proposed solution to the above paradox leads to a new evolutionary picture, where progress is not a result of successful accumulation of mistakes in replication of the genetic code, but is rather the outcome of designed creative processes.
This guy really likes that strawman argument. He sets up one false dichotomy after another. The question is not creativity but diversity. Without diversity evolution would fail for the simple reason that the real life tests are often similar to the Luria and Delbrck experiment. With diversity there is no need to postulate creativity, which begs the question (again in usual ID fashion) of needing a creative agent.
.... since they showed that the genome is a dynamic entity capable of changing itself. These are a fundamental to our new picture of the genome. ... My belief in cooperative genetic changes led me to a new experimental endeavor, in which the selective pressure was on the colony. The new experiments led to important new observations ... of morphotype transitions in stressed colonies. These are genetic changes which are beneficial to the colony but not directly to the individual cells.
And seeing as evolutionary natural selection operates on the diversity of species rather than specific individuals this result is not surprising, but the conclusion appears to be pre-assumed and not due strictly to the evidence.
The new picture of the genome as an adaptive cybernetic unit with self-awareness ... The genome, as I see it, is not merely a storage device, but a sophisticated cybernetic entity well beyond a universal Turing machine. Metaphorically speaking, it includes a user, a computational unit, and a hardware engineer and technicians. ... during computations the structure is dynamic and changes adaptively according to the needs dictated by the computations. The crucial component is the ``user'' which can recognize difficulties imposed by the environment and formulate problems requiring solution. ... I further assume that the genome has self-awareness.
He goes on to attribute supernatural abilities to this "user" ... in all, some pretty spectacular claims ... we'll see if they pan out.
At first it seems that the assumption that the genome is an adaptive cybernetic unit with self-awareness will suffice to explain evolution ... Gdel's theorem ... Naively phrased, it says that a system cannot design another system which is more complex than itself.
Naive or just another strawman argument? By this argument, stellar gas can never condense into solar systems and fractal images can never develop from simple equations.
I use the distinction between Kuhn's normal science (problem solving within the scientific paradigm) and scientific revolutions (creation of a new scientific paradigm) as a metaphor to define horizontal genomic changes vs. vertical genomic leaps. The extension of Gdel's theorem would imply that the genome is not capable of performing genomic leaps. Yet these may be the most relevant changes in evolution.
Are we back to random mutations? Could it be that the horizontal genomic changes are self designed changes in response to the environment, and the more dramatic vertical genomic leaps are due to Darwinian evolution? I don't think so, and suggest the new picture of cooperative evolution as an alternative.
Perhaps he should use "micro" and "macro" instead of "horizontal" and "vertical" ... it would be more familiar terminology to the audience. The distinction between "allowed change" and "not allowed change" is equally false as well.
Section 1
The experiments did prove the existence of random mutations, but it did not rule out the possibility that there are also non-random mutations. Nevertheless, these experiments were taken as a support of the Neo-Darwinian dogma which states that all mutations are random, and occur only during DNA replication.
Now he attacks Neo-Darwinism as a basis of evolution? The last statement is patently false: mutations occur on a steady basis, translation errors can only occur during replication, but translation errors are not mutations, and may be caused by pollutants in the cell or pre-existing mutations in the operon sections of the DNA.
Section 2
The regulatory genes and the theory of the operon (a number of genes that function coordinately under the control of a regulatory gene) were proposed by Jacob and Monod in 1961. This is one of a number of great discoveries during the 50's which should have shattered the picture of a static genome which serves as a storage unit only.
Shattered what picture? These operons would only be analogous to the "DO WHILE" or "IF THEN" sections of programming code, which was the dominant (and still is?) image of DNA in the 50's.
The plasmids ... are double-stranded, closed DNA molecules ranging in size from 1 to 200 Kbars. Plasmids can be integrated into the host chromosome. Their replication is either autonomous or coupled to that of the host. The number of plasmids per host cell may be from 1 to 100. The plasmids can be used to transfer DNA sequences between cells. Some can initiate conjugation (a temporary union of two cells for exchange of genetic materials), some can be transferred during conjugation, and others can help transfer non-mobilizable plasmids.
This looks like the mechanism by which DNA "information" has been transferred by cells (if not proto-cells) since time began. This is also involves the method used by viruses to invade a cell and commandeer the production factories. Because of this ability of cells to exchange "information" there is a theory that several forms of the first cells to evolve combined forces to result in an improved product at the earliest opportunities, and another that the mitochondria is a remnant of an invading cell kept by the host and used in the ultimate symbiotic relationship. This is still just "information" exchange at the used book counter.
In 1954 Ryan demonstrated that genetic changes can occur not during replication ... provided the bacteria with food they cannot "digest" and low level of digestible food, insufficient for the bacteria to replicate. He observed the appearance of new mutants that could digest the food, which indicated genetic changes not during replications.
The above findings, put together, should have led to a new picture of a dynamic genome, but did not. Today the genome is still defined simply as the collection of all genes carried by a single gamete ...
We have already discussed the falsity of mutation only during replication. These precepts for a "new picture of a dynamic genome" are false, and so any conclusion based on them must also logically be false (or unjustified).
I propose a new picture of the genome as an adaptive cybernetic unit with self awareness. In this picture the genome includes the chromosome, all the extra-chromosomal elements and all the ``chemical machinery'' (like enzymes) involved in genomic activity and the production of proteins. ... 'element' is misleading, as those are actually agents. I further propose to refer to them as cybernetic agents, or cybernators. My new picture is based also on the known abilities of the genome to change itself ...
It has been pointed out that redefining words to new definitions leads to confusion. He is free to invent a new term (as he does with "cybernator" ...
but will it run for governor?).
Actually what he is talking about is the cell. And "... known ... to change itself ..." implies an active hand where none has been demonstrated (see diversity versus creativity discussion above). And if he means "agent" then why have "element" at all in the presentation? He seems confused.
Section 3
... They showed that a specific mutation will occur in high frequencies only when needed to remove the selective pressure, i.e. during a selection for that mutation and not in other stressful conditions, and that the former selection, which triggers the specific mutation, does not trigger other mutations. Cairns et al. concluded that those mutation were adaptive, i.e. that the bacteria somehow mutate in order to adapt to the selective pressure. These experiments and the conclusions triggered a furious debate in the biological community and led to various additional experiments. The latter ruled out several more conventional interpretations, and showed the active role of the bacteria in the events of adaptive mutations ...
Or it just showed that the bacteria were able to switch from a low level of mutation to a higher level of mutation when stressed. A high level during normal situations can be disadvantageous as it creates additional competition, so it could be a real advantage to switch between different levels of mutation for different levels of stress. This does not imply any conscious switching, nor proactive, just reactive. Again, this is nothing more that a "DO WHILE" or "IF THEN" kind of program feature.
One of the most interesting set of experiments related to this subject is Hall's experiments of double mutations [24,25]. In those experiments two mutations in two genes were needed to enable bacterial growth. The most important feature of the results is the doubling of the delay time preceding the appearance of the adapted mutants.
{24. B. G. Hall. Adaptive evolution that requires multiple spontaneous mutations. i. mutations involving an insertion sequence. Genetics, 120:887--897, 1988.}
{25. B. G. Hall. Adaptive evolution that requires multiple spontaneous mutations: mutations involving base substitutions. Proc. Natl. Acad. Sci. USA, 88:5882--5886, 1991.}
Well, here we have the reference to Hall you mentioned. Not much about them here (he doesn't discuss the "Irreducible Complexity" issue as it doesn't involve his thesis), but the references should enable us to track down the actual documents.
Recent experiments by Galitski et al. and Radicella et al. began to confirm Ben-Jacob et al. [21] hypothesis, that in order to perform adaptive mutations (and other non-random mutations) the bacteria employ cybernetics elements ...
{21. E. Ben-Jacob, H. Shmueli, O. Shochet, and A. Tenenbaum. Adaptive self-organization during growth of bacterial colonies. Physica A, 187:378--424, 1992.}
Is it me or is the use of your own work in an article to justify your conclusions of your own work just a little bit circular (if not downright cheesy)?
Section 4 - Colonial stress and morphotype transitions
It is now understood that bacteria paved the way for life on Earth as we know it, ... Only recently have the notions of smart bacteria and bacteria as multicellular organism (both with respect to bacterial colonies) started to gain attention. Armed with the new developments in the study of patterning in non-living systems, I set out to promote the above notions.
(cue
Startrek theme ... )
He set out to prove his assumption, not to test it? Baaad sign. Very bad sign. And this section is supposed to be the meat of the article, the wheat buried in the chaff (and there certainly has been chaff) ....
The study of diffusive patterning in non-living systems teaches us that the diffusion field drives the system towards decorated irregular fractal shapes. Hence, I expected complex patterns to be developed by nutritionally stressed colonies. We have created such hostile growth conditions in a petri dish by using low levels of nutrients and a hard thin substrate (high agar concentration). Indeed, we observed some very complex patterns.
Fractals as a basis for complexity of design? Okay ... but nothing new shown here: "very complex patterns" just means that there is not a consistent pattern of growth, which is what should be expected from such a stressing environment.
Moreover, the colonies exhibit richer behavior than patterning of non-living systems, reflecting the additional levels of complexity involved ...
Umm,
duh?
The building blocks of the colonies are themselves living systems, each having its own autonomous self-interest and internal degrees of freedom. At the same time, efficient adaptation of the colony to adverse growth conditions requires self-organization on all levels -- which can only be achieved via cooperative behavior of the individual cells.
Colonies are already symbiotic in their interrelationships, adding stress to a colony does not change this element of pre-existing behavior. The colony will continue to use the resources and output of living members whether stressed or not stressed.
To achieve the required level of cooperation, the bacteria have developed various communication capabilities, such as: 1) direct cell-cell physical and chemical interactions, 2) indirect physical and chemical interactions, e.g., production of extracellular "wetting" fluid, 3) long range chemical signaling, such as quorum sensing, and 4) chemotactic signaling (chemotactic response to chemical agents which are emitted by the cells).
As noted previously they already have symbiotic interrelationships, and these interactions are nothing more spectacular than the "DO WHILE" and "IF THEN" type of responses to stimuli and stress as previously discussed.
Had we demonstrated ... inherited colonial ... characters resulting from environmental stress on the colony... it would provide strong support to the notion of bacterial colonies as a multicellular organism. ... we set up experiments with the above special goal in mind. The working hypothesis was that transitions were expected from a morphotype (a colonial geometric character which is inherited and can be carried by an individual bacterium) which expands slowly to a faster expanding one. This means that the colony which can propagate faster on the agar surface has an advantage in reaching the food. Transitions between two of the morphotypes we have identified the tip-splitting {T} and the chiral {C} morphotypes have been observed. As expected, we observed {T to C} transformations on softer surfaces for which {C} is the faster morphotype, and the reverse {C to T} transformations on harder surfaces on which {T} is the faster one. ...
(Excuse me while I stop chuckling) ... we have already seen that in a bacterial colony there are members that take on differentiation of tasks, some specializing in some things others doing other tasks. Now we see that two differentiated types have pre-adapted differential survival ability to different environments. Is this really a surprise? Is it news? No. At best this is no different from the result in section 3 above except that there is some existing pre-adapted diversity maintained by the colony, and no effort appears to have been made to control for that.
... Since the growth velocity is a colonial property, our observations indicate that some selective colonial pressure is invoked. This would be an extension to living systems of the "fastest growing morphology" selection principle.
Now we are facing two riddles. One is the manner in which colonial pressure can reach down to the single bacterium and cause genetic changes in the individual cells such that a transformation from the {
T} type to the {
C} type occurs. ...
But that is not what is demonstrated, just that there are more of one type in one situation and more of the other type in another. There is preferential survival in response to the environment and this allows more of one type or the other to survive and reproduce ... and to become the dominant type in the colony.
Another, related riddle has to do with the morphotype bursts. Sparse cells of the {C} morphotype scattered among the {T} cells within a {T} colony have no individual advantage and no effect on the colonial structure even during growth on soft substrate for which the {C} morphotype is the preferred one. Only finite nucleation of the {C} cells has an advantage (on soft substrate), as it can lead to a burst of the preferred morphotype
Perhaps because the {
T} type is not stressed by the "soft" environment the way the {
C} type is by the "hard" environment. Or the {
T} type is the preferred (dominant) type. In either case, it is not a riddle any more than the other was, more like finding pre-assumptions like seeing "pictures" in pieces of french toast.
One possible ... is that of autocatalytic or synchronized genetic changes. If so, a mechanism for such changes needs to be proposed.
Or any other possibility can be developed instead. Such as given above.
That is the end of the "nuts and bolts" section, and it fails to measure up to the promised demonstration of supernatural ability in the microcosmic universe.
Do you want me to continue or have we had enough?
background color changed due to complaints
This message has been edited by RAZD, 12-20-2004 10:23 PM
we are limited in our ability to understand
by our ability to understand
Rebel
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