Microbial Versatility

Why microbes are smarter than you thought is a New Scientist article containing subtopics of interest. There are also multiple links within the article.

This entry was posted on Wednesday, July 1st, 2009 at 10:26 am and is filed under Biology, Science. You can follow any responses to this entry through the RSS 2.0 feed. Both comments and pings are currently closed.

29 Responses to “Microbial Versatility”

Bradford Says:
July 1st, 2009 at 1:19 pm
During the early 1990s, researchers suggested that bacteria might have a way to "choose" mutations that would be particularly useful. This idea of directed mutation was extremely controversial, and by 2001 the evidence was stacked against it (Nature Reviews Genetics, DOI: 10.1038/35080556).

Although the concept was not establshed by the data, directed mutations can be viewed as processes that enable front loaded outcomes. There were parallel questions raised in Bilbo's ribosome thread.

Comment by Bradford — July 1, 2009 @ 1:19 pm

The Pixie Again Says:
July 1st, 2009 at 3:20 pm
I love how "by 2001 the evidence was stacked against it" becomes "Although the concept was not establshed by the data".

Comment by The Pixie Again — July 1, 2009 @ 3:20 pm

Bert Says:
July 1st, 2009 at 3:36 pm
But many bacteria and protists also exhibit behaviour that looks remarkably intelligent. This behaviour isn’t the result of conscious thought – the sort you find in human and other complex animals – because single cell organisms don’t have nervous systems, let alone brains.

A better explanation is that they’re “biological computers” with internal machinery that can process information.

This article makes the materialist error of equating mind with brain. If mind doesn’t take up space, there is no limit to where it might exist. Understandably, materialists are more optimistic about finding a tiny computer in single cell organisms. That is the eternal materialist quest, and I wish them luck. We non materialists know that physical traces of mind will never be found – they don‘t exist. It is understandable that materialists should deny the existence of something lacking a physical component. They argue that the apparent creativity of nature is an illusion – just a series of accidents that “natural selection“ somehow renders creative.

So which drives living systems – a “biological computer” or mind? There are clues which might help us to hazard a guess. Computers and deterministic systems are all or nothing. The response is automatic, and predictable. Mind driven mechanisms always vary and are only statistically predictable. Mind is capable of purposeful creativity. Artificial intelligent aficionados are convinced a computer equal to a brain is possible. However no one has even suggested a computer exhibiting initiative – creative, purposeful response to unforeseeable conditions. So far as we know, purposeful creativity is an ability limited to mind and living biological systems. We might deny the creativity of nature, but I would have a hard time denying the reality of my own mind.
bertvan
http://30145.myauthorsite/com/

Comment by Bert — July 1, 2009 @ 3:36 pm

chunkdz Says:
July 1st, 2009 at 4:11 pm
Pixie: I love how "by 2001 the evidence was stacked against it" becomes "Although the concept was not establshed by the data".

Actually, both are misleading. The phenomenon was simply relabeled as "adaptive mutation".

Comment by chunkdz — July 1, 2009 @ 4:11 pm

hrun Says:
July 1st, 2009 at 4:26 pm
This article makes the materialist error of equating mind with brain. [...]

Bert, did you read any of the primary literature that the examples of the article are based on? Did you familiarize yourself with all the basic science? And did you actually notice how many of these examples of bacterial 'smarts' are actually well defined 'thermostat type' (as you call them) mechanisms?

Or did you just give a response that was 'automatic, and predictable'?

Comment by hrun — July 1, 2009 @ 4:26 pm

themayan Says:
July 1st, 2009 at 5:02 pm
Bacteria are some of the most mysterious and complex biological sytems that we know of next to slime balls, not bad for what some consider one of the most primordial domains of life, especialy when comparing diversity and c values. I have had many discussions with those who use automatan theory as scientific evidence for the hypothesis that inanimate molecues over time can eventually become Albert Einstiens and the likes. They say it can be demonstrated through complex computer programs. Unfortuantly it can only be demonstrated in virtual worlds that are based on unrealistic non biological criteria, and they always fail to understand that it took a computer programer to program the program. Ive always found this logic almost as facinating as the theory itself. The failure to seriously consider and recognize the fundamental causation of information in these models, is like the ostridge who buries his head in the sand and all you can see is his backside. Me also thinks its a weasel…..or ostridge?

Comment by themayan — July 1, 2009 @ 5:02 pm

Bert Says:
July 1st, 2009 at 5:31 pm
Bert, did you read any of the primary literature that the examples of the article are based on? Did you familiarize yourself with all the basic science? And did you actually notice how many of these examples of bacterial 'smarts' are actually well defined 'thermostat type' (as you call them) mechanisms?

Hi hurn, I read all your material and am still unconvinced of the thermostat type explanation. Even when some of the details of the process are discovered, something triggers the response. It looks more like a purposeful choice response rather than an automatic, deterministic one to me. Signaling, for instance. The medium is not the signal, any more than sound waves are the message in vocal signals. Something interprets the signal, evaluages the message, and determines the response. I interpret those chemicals as signals. Deterministic reactions would be constant and uniform, and I suspect these are not.
bertvan
http://30145.myauthorsite.com/

Comment by Bert — July 1, 2009 @ 5:31 pm

hrun Says:
July 1st, 2009 at 5:49 pm
Even when some of the details of the process are discovered, something triggers the response. It looks more like a purposeful choice response rather than an automatic, deterministic one to me.

Bert. How is this a matter of opinion? I simply do not understand. If we had an actual thermostat, is there any way in your opinion how we could actually ascertain if it is deterministic rather than purposeful?

Something interprets the signal, evaluages the message, and determines the response.

Yes, exactly. Something does this. In this case, the message is 'lactose is there', this information gets received by the lac repressor and the predetermined response is to cease DNA binding (which in turn allows the lac operon to be transcribed).

It's all there, down to the molecular detail– exactly like my thermostat at home.

Deterministic reactions would be constant and uniform, and I suspect these are not.

And there, you did it again. You had me actually believing that you had tried to familiarize yourself with the material… and yet, there it is for everybody to read: you suspect. No suspicion is needed. Look at the thousands of experiments that have been done and figure out if they are or are not 'constant and uniform'.

It is just so disappointing. On the one hand you appear receptive, yet, you just refuse to do any work– you'd just much rather 'suspect' or 'believe' stuff so it continues to fit in your world view. Very disappointing indeed.

Comment by hrun — July 1, 2009 @ 5:49 pm

Bert Says:
July 1st, 2009 at 6:51 pm
.. Is there any way in your opinion how we could actually asertain it is deterministic rather than purposeful?

Hi Hrun, probably not to everyone’s satisfaction. There have always been materialists and non materialists, and I assume there always will be. When it comes to the important questions such as the difference between mind and brain, whether or not living systems interact deterministically or purposefully, the existence of possible deities, whether intelligence interacts with reality – science has no priority. We each bring all our life experiences to formulating a conclusion. Scientists are as susceptible to prejudice as the rest of us. I have no desire to change your conclusions. I actually find your posts, though sometimes unpleasant, a very real stimulus to developing my non deterministic, non materialist thoughts. So thanks again for the comment.

As to your lactose example. Does the lactose directly enter into a direct chemical reaction with the nucleotides in the genome. I have no way to deny it, so I accept it. That still would not explain how such adaptations might happen in multi celled organisms where no specific chemical is known to interact chemically with the genome, which is isolated in the nucleus of the cell. And as far as I’m concerned it wouldn’t explain the foloowing:

http://www.newscientist.com/article/mg20227141.600-review-wetware-by-dennis-bray.html

squirt a jet of an irritant chemical and the cells will arch its stalk-like body out of the way, moving from side to side to avoid the stream. If this fails it retreats. If the chemical is still there when it emerges, it retreats again. .

This sounds to me more like purposeful, creative behaviour than like a deterministic chemical reaction. Chemical reactions are uniform, rather than varied.

. .living cells, like the single celled protozoa pictured are chemical computers. They take information from the environment and process it to produce behavioural “outputs”.

Proponents of artificial intelligence might envision computers that show initiative, but like the origins of life researchers, nothing has happened so far. Computers do what they are programmed to do. Innovation and purposeful creativity is beyond them. All the evidence suggests to me that living systems produce purposeful, creative behaviour rather than interacting by deterministic, uniform, inorganic chemical reactions
bertvan
http://30145.myauthorsite.com/

Comment by Bert — July 1, 2009 @ 6:51 pm

hrun Says:
July 1st, 2009 at 9:01 pm
As to your lactose example. Does the lactose directly enter into a direct chemical reaction with the nucleotides in the genome. I have no way to deny it, so I accept it.

Okay, Bert, I am done with you. You are simply wasting my time. First you claim to have read my links and explanation and there you are talking about lacrtose interacting directly with the nucleotides of DNA. I have summarized it multiple times and I have pointed you to the Wikipedia site and the primary literature. It's absolutely embarrassing that you have still not grasped even the basics about how lactose regulates the lac operon.

And this is not a matter of opinion or belief. You have simply not informed yourself about what is know and how it is known.

I'll say this one last time: You have not even reached high school level biology, but you make these sweeping pronouncements. You revel in your ignorance, because actually informing yourself might pose a challenge to your beliefs.

Comment by hrun — July 1, 2009 @ 9:01 pm

hrun Says:
July 1st, 2009 at 9:06 pm
And just as a final example:

And as far as I’m concerned it wouldn’t explain the foloowing:[...]

Again, sweeping statemets about what it would and would not explain. But not even a basic effort to inform yourself about what is actually known about these processes. Embarrassing.

Comment by hrun — July 1, 2009 @ 9:06 pm

Raevmo Says:
July 2nd, 2009 at 5:19 am
themayan:

they always fail to understand that it took a computer programer to program the program. Ive always found this logic almost as facinating as the theory itself.

Your fascinating statement is typical of those who have a fundamental inability to grasp the concept of a model, in a sadly Gil Dodgenian kind of way. According to your logic, the fact that an intelligent being like Einstein formulated the equations of general relativity somehow implies that planetary orbits require an infusion of information by an intelligent designer.

Comment by Raevmo — July 2, 2009 @ 5:19 am

Bradford Says:
July 2nd, 2009 at 11:07 am
the mayan: they always fail to understand that it took a computer programer to program the program. Ive always found this logic almost as facinating as the theory itself.

Raevmo: Your fascinating statement is typical of those who have a fundamental inability to grasp the concept of a model, in a sadly Gil Dodgenian kind of way. According to your logic, the fact that an intelligent being like Einstein formulated the equations of general relativity somehow implies that planetary orbits require an infusion of information by an intelligent designer.

While Einstein's descriptive formulas say nothing about the origin of mass and energy his use of symbols, to represent physical entities and their relationships to each other, can be viewed as an indicator that symbols owe their source to a desgner.

Comment by Bradford — July 2, 2009 @ 11:07 am

Bert Says:
July 2nd, 2009 at 11:17 am
“Most people are really hung up on this idea that intelligence is limited to humans.”

These are not my words. A fully qualified scientist believes intelligence is not limited to humans. Furthermore, he believes such a limited notion of intelligence is a “hang up”.
http://www.newscientist.com/article/mg14719953.500-the-secret-language-of-bacteria.html?page=3

Understanding the chemical chatter of bacteria is just the start. Under attack is the whole deep-seated notion of bacteria as dumb cells that act robotically on information in their DNA. Chemical crosstalk, claim today’s microbiologists, enables bacterial cells to cooperate in ways approaching in ways approaching the complexity of animal communities; to specialize like those multi cellular organisms; to behave socially.
.
. ..what they believe they are discovering is a chemical and genetic language reminiscent of the one that guides the embryonic development of multi cellular organisms.

.Don’t confuse the message with the medium in which it is conveyed. A message conveyed by a chemical doesn’t necessarily mean that the chemical carries out the action conveyed by the chemical message

. . .Shapiro even uses the term “sentient“ to describe the way some bacteria mutate in an apparently non-random manner.
. . .Davies even considers bacteria “emotional“, in the sense that like people they have needs which they act to satisfy. .
When Frisch’s work hinted that bees can communicate in an intelligent manner, it took decades of experiments for others to agree. Achieving that kind of recognition for micro-organisms may prove even ore difficult. “Most people are really hung up on the idea that intelligence is limited to humans,” says Shapiro. “We assume that bacteria are rather simple, rather primitive and rather limited. I think that is to our detriment.”

Actually, I doubt that the average layman is that “hung up”. Only those biologists who have spent a lifetime trying to defend RM&NS have an emotional reaction to the idea of intelligence in nature.
bertvan
http://30145.myauthorsite.com/

Comment by Bert — July 2, 2009 @ 11:17 am

Raevmo Says:
July 2nd, 2009 at 12:24 pm
Bradford:

While Einstein's descriptive formulas say nothing about the origin of mass and energy his use of symbols, to represent physical entities and their relationships to each other, can be viewed as an indicator that symbols owe their source to a desgner.

The fact that humans design models (mathematical or computer simulations) to describe phenomenon X does not imply at all that X must have been designed, contrary to what our Mayan friend seemed to suggest.

Also, the fact that Einstein used symbols in his models says not much about symbols in general, does it? Of course you are referring to nucleotide triplets being "symbols" for amino acids, but there are actually plenty of such symbols in nature that have a perfectly acceptable naturalistic explanation, so you would have to show why the genetic code is special in that regard.

Comment by Raevmo — July 2, 2009 @ 12:24 pm

Raevmo Says:
July 2nd, 2009 at 12:31 pm
Bert:

Actually, I doubt that the average layman is that “hung up”. Only those biologists who have spent a lifetime trying to defend RM&NS have an emotional reaction to the idea of intelligence in nature.
bertvan

Very weird claim. (1) What biologists spent a lifetime "defend" RM&NS? (2) What biologists have an emotional reaction to the idea of intelligence in nature, when it's not controversial at all that all animals, and even plants and protists are intelligent to some degree? I think you are attacking a strawman of your own creation.

Comment by Raevmo — July 2, 2009 @ 12:31 pm

Bradford Says:
July 2nd, 2009 at 12:57 pm
Raevmo: Of course you are referring to nucleotide triplets being "symbols" for amino acids, but there are actually plenty of such symbols in nature that have a perfectly acceptable naturalistic explanation, so you would have to show why the genetic code is special in that regard.

There is variation in symbols but the key question in my view is whether or not a symbolic system would be the consequence of physical necessity grounded in natural laws or whether physical constraints indicate an intelligent source.

Comment by Bradford — July 2, 2009 @ 12:57 pm

Bert Says:
July 2nd, 2009 at 3:31 pm
What biologists spent a lifetime "defend" RM&NS? (2) What biologists have an emotional reaction to the idea of intelligence in nature, when it's not controversial at all that all animals, and even plants and protists are intelligent to some degree? I think you are attacking a strawman of your own creation.

Hi Raevmo, I'm delignted to hear I might be attacking a strawman. However I haven't had any trouble finding people who defend "natural selection" as the force behind evolution, and also people who regard attributing intelligence to anything other than humans as "anthropomorphic". If intelligence of any form is involved in living processes, then life is intelligently designed. Right? And ID has been accepted. Meanwhile, here is a scientist with whom we apparently have no disagreements.

http://shapiro.bsd.uchicago.edu/index3.html?content=genome.html

Central dogma revisited, 2008
When the structure of DNA was figured out in 1953, there was a strong belief among the pioneers of the new science of molecular biology that they had uncovered the physico-chemical basis of heredity and fundamental life processes. Following the discoveries about the process of protein synthesis, the consensus view most cogently summarized a half a century ago in 1958 (and again in 1970) by Crick’s declaration of “the central dogma of molecular biology.” The concept was that information basically flows from DNA to RNA to protein, which determines the cellular and organismal phenotype. While it was considered a theoretical possibility that RNA could transfer information to DNA, information transfer from proteins to DNA, RNA or other proteins was considered outside the dogma and “would shake the whole intellectual basis of molecular biology.” This DNA/nucleic acid-centered view is still dominant in virtually all public discussions of biological questions, ranging from the role of heredity in disease to arguments about the process of evolutionary change. Even in the technical literature, there is widespread assumption that DNA, as the genetic material determines all action and that the observed deviation from strict genetic determinism must be the result of stochastic processes.

The idea of a “dogma” in science has always struck me as inherently self-contradictory. . . .The great irony of molecular biology is that it has led us inexorably from the mechanistic view of life it was believed to confirm to an informaic view that was completely unanticipated by Crick and his fellow scientific pioneers.

Since you have no objection to viewing intellience as an aspect of biolobical organization, you would have no objection to the substitution of 'intelligence driven' for 'informaic' in the above quotation, right?
bertvan
http://30145.myauthorsite.com/

Comment by Bert — July 2, 2009 @ 3:31 pm

themayan Says:
July 4th, 2009 at 3:27 am
Ravemo.. yes you are accurate in your assumptions, I do believe in an anthropic cyclematic universe. I have never seen any evidence of a chaotic event, whether a big or small bang that can produce order. The notion of chaos producing order is a fairytale of the highest order. I think there are many, including atheist and agnostics who recognize the fine tuning of the cosmos. Even Dawkins has admitted to scratching his head on that one. I believe old Albert also believed in some kind of esoteric higher power. If you have a theory for the accountability of complex information that can be demonstrated empirically, I would love to hear about it, and I mean that only half sarcastically and the other half sincerely.

Comment by themayan — July 4, 2009 @ 3:27 am

Raevmo Says:
July 4th, 2009 at 8:40 am
themayan:

I have never seen any evidence of a chaotic event, whether a big or small bang that can produce order. The notion of chaos producing order is a fairytale of the highest order.

You seem to consider your own deep ignorance as evidence. Have you ever heard of Statistical Mechanics, the branch of physics that studies how chaos at the microscopic level causes regularities at the macroscopic level? I guess not. You might like some books by Prigogine, such as Order out of Chaos: Man's new dialogue with nature.

Comment by Raevmo — July 4, 2009 @ 8:40 am

themayan Says:
July 4th, 2009 at 5:09 pm
Ravemo The fundamental Postulate of Statistical Mechanics is still regarded as a frame work based on assumption, where as classical thermodynamics can be demonstrated empirically. However if you feel that this theory is sufficient to satisfy your intellectual curiosity dont let my ignorance stop you.

Comment by themayan — July 4, 2009 @ 5:09 pm

Todd Berkebile Says:
July 4th, 2009 at 5:23 pm
mayan,

Hehe, you read that page and all you came away with is that the word "assumption" was used. I just can't understand why ID supporters have yet to accomplish anything.

Comment by Todd Berkebile — July 4, 2009 @ 5:23 pm

themayan Says:
July 4th, 2009 at 7:13 pm
Tod I suggest you look at the history of western science and you will find names like Copernicus,Gallileo,Pasteur,Newton,Mendel,Fermi and a whole host of scientist who believed in design, many of these men accomplished great discoveries and insights that make up the modern synthesis of many fields of scientific disciplines. This is what separates empirical science from historic and hypothetical scientific inquiry. Evolution, Pangenes, Panspermia,Exobiology,abiogenesis etc.

Comment by themayan — July 4, 2009 @ 7:13 pm

Todd Berkebile Says:
July 4th, 2009 at 9:31 pm
Tod I suggest you look at the history of western science and you will find names like Copernicus,Gallileo,Pasteur,Newton,Mendel,Fermi and a whole host of scientist who believed in design, many of these men accomplished great discoveries and insights that make up the modern synthesis of many fields of scientific disciplines.

Uh, yeah, so? This relates to what we are talking about how?

This is what separates empirical science from historic and hypothetical scientific inquiry. Evolution, Pangenes, Panspermia,Exobiology,abiogenesis etc.

So you think belief in god is required to perform "empirical science"? But evolution isn't science even though many religious scientists have contributed to the theory? Do you even know how to maintain a train of thought? Do you actively strive to avoid self consistency?

Comment by Todd Berkebile — July 4, 2009 @ 9:31 pm

themayan Says:
July 5th, 2009 at 12:34 am
Tod your ability to distort the context is exceptional. I'm not sure we would agree on much, but if you ever decide to become a lawyer I would hire you in a second. OJ couldn't have done better job. Tod your an interesting fellow but can we drop the your so dumb insults, or at least make them entertaining, sprinkle them with a little sunshine. Lighten up, sometimes all we really need is a bran muffin.

Comment by themayan — July 5, 2009 @ 12:34 am

Raevmo Says:
July 5th, 2009 at 6:22 am
themayan:

Ravemo The fundamental Postulate of Statistical Mechanics is still regarded as a frame work based on assumption, where as classical thermodynamics can be demonstrated empirically. However if you feel that this theory is sufficient to satisfy your intellectual curiosity dont let my ignorance stop you.

Classical thermodynamics breaks down empirically in small systems precisely because the chaotic motions of particles do not cancel out statistically. Don't worry mate, I'll just laugh at your combination of ignorance and arrogance that is so typical of the deluded.

Comment by Raevmo — July 5, 2009 @ 6:22 am

themayan Says:
July 5th, 2009 at 8:39 am
I quoted from the article you cited which is a very complex set of theoretical and quantum mathematics that deal with complex equations statistical probabilities, imaginary time fluctuations, entropy slopes, and equilibrium etc. if you understand it fully then bravo, I'm not as bright as you, again I was citing your own reference. You made the statement that entropy breaks down empirically in small systems. Is this your opinion can you cite a source that substantiates the empirical nature of this theory. If there is such a thing as a sub atomic entropy hole that even directional energy could not compel, then how does that necessarily negate decay and the continual tendency towards chaos over time? The universe will still eventually suffer a heat death and uniformity in temperature with no usable energy left.

Comment by themayan — July 5, 2009 @ 8:39 am

Todd Berkebile Says:
July 5th, 2009 at 12:33 pm
mayan: Tod your ability to distort the context is exceptional.

I'll take this to mean you won't be answering any of the questions asked of you in order to clarify your rather confusing statements.

PS: And this time I will refrain from mentioning any psychological conditions that your behavior is a perfect example of.

Comment by Todd Berkebile — July 5, 2009 @ 12:33 pm

themayan Says:
July 5th, 2009 at 6:58 pm
Tod…Thank you for showing mercy on little old me. You are truly a benevolent genius, I'm not sure if I rightly comprehend big words like psychological condition but since your such a sweet heart I'm sure it means something nice and warm, but for the sake of others, why dont you give an example of your understanding on the finer and more complex points of quantum physics and Statistical Mechanics.

Comment by themayan — July 5, 2009 @ 6:58 pm

Microbial Versatility

29 Responses to “Microbial Versatility”

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