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Author Topic:   Does the Darwinian theory require modification or replacement?
Taq
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Message 8 of 760 (609067)
03-16-2011 11:18 AM
Reply to: Message 1 by shadow71
03-15-2011 4:03 PM


I propose that we are now entering into a new era of the theory of Evolution. This may be called the Information driven theory, the Bio-Communicative theory, the Cell Intelligence theory of Evolution, or whatever appropriate name fits the theory.
I started a career in microbiological research 15 years ago. In that time I have seen a huge improvement in the technology used to study molecular biology. For example, in the mid 1990's it was not unheard of for a grad student to spend 3 years sequencing the genome of a single bacterium (3-5 million bases) as their graduate project. It was "slow" (compared to now), laborious work. The human genome project was ongoing when I was in high school, almost 20 years ago, and finished in 2003. Since that time automation and new techniques have allowed the sequencing of a bacterial genome in a single day and the sequencing of a human genome in 3 months. The same sort of improvements have been made across the board, such as the ability to measure the regulation of tens of thousands of genes simultaneously from a single sample. This increase in data has led to a real revolution in research, and it is still ongoing.
As far as theory, the biggest change I have seen is Evolutionary Developmental Biology, or Evo-Devo as it is often called. Early in the development of the Modern Synthesis there were some who thought that one feature equalled one gene. That was wrong. The adaptations we see are the result of many genes interacting in regulatory networks. The evolution of this process is very important for understanding the evolutionary history of the modern animal species that we see. Evo-Devo also has some of the coolest sounding genes, such as the tinman gene that is involved in heart development (reading a paper on that right now).
Should the Modern Synthesis change? Of course. It has not stopped changing in the last 70 years. It will continue to change. It has to change. Will we need to chuck the theory altogether? No one has found a reason to yet. The fundamentals of the theory are still widely accepted: mutations are blind to fitness and natural selection is blind to sequence and design. Even Shapiro agrees with this fundamental tenet of the Modern Synthesis. The rest are just details which do change over time.
Edited by Taq, : No reason given.
Edited by Taq, : grammar

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 Message 1 by shadow71, posted 03-15-2011 4:03 PM shadow71 has replied

Replies to this message:
 Message 12 by slevesque, posted 03-16-2011 1:52 PM Taq has replied
 Message 18 by shadow71, posted 03-16-2011 4:42 PM Taq has replied

Taq
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Member Rating: 5.6


Message 14 of 760 (609094)
03-16-2011 3:05 PM
Reply to: Message 12 by slevesque
03-16-2011 1:52 PM


I agree with shadow71 here that, hypothetically speaking, if mutations were to be shown to be none-random in that outside stimuli can produce the right mutations for adaptation, this would be a much more profound change to the fundamentals of the theory then pretty much everything since the synthesis.
The fact is that mutations have been demonstrated to be random with respect to fitness. Even the mutational processes that Shapiro cites are random with respect to fitness. A transposon is not capable of determining which insertion point would be helpful to the organism. They insert all over the place. These insertions can and are beneficial, neutral, and detrimental. Secondarily, natural selection does not choose between transposon insertions based on their placement within the genome. Natural selection is based on the effect of that insertion on the overall fitness of the organism. The two are disconnected, which is the basis of the Modern Synthesis.
Edited by Taq, : No reason given.

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Taq
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Posts: 9972
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Member Rating: 5.6


Message 17 of 760 (609102)
03-16-2011 4:29 PM
Reply to: Message 15 by slevesque
03-16-2011 3:48 PM


Yeah well I perfectly understand that, I was just saying that hypothetically speaking, what shadow71 proposes would entails a drastic revision, not simply 'details'
At this point, such observations would be limited to very special cases. Is it possible that there is a very rare bacteria, found in the soil of southern Italy, that changes one base in one gene in response to the presence of a phosphorylated protein released by another very rare fungus? I suppose this is possible, but once again this would be a very special case. It is not the norm. Experiment after experiment has demonstrated random mutation for a very wide variety of mechanisms, even those spoken of by Shapiro.
So would finding a few specific and special cases of guided mutation throw out all of the mountains of data demonstrating random mutation? I would say no. The special cases are footnotes. Even comparisons of genomes demonstrates different rates of synonymous to non-synonymous changes, hallmarks of random mutation and selection. Do we throw out a theory that describes 99.99999% of the evolutionary history of genomes because that 0.00001% is guided by environment? Again, I would say no.

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Taq
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Posts: 9972
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Message 21 of 760 (609107)
03-16-2011 5:01 PM
Reply to: Message 18 by shadow71
03-16-2011 4:42 PM


It appears to me that he is saying that the suddent abrupt changes are nonrandom and performed by natural genetic engineering.
All of this hinges on how Shapiro defines "nonrandom" as it relates to the process of mutation. Unfortunately, Shapiro defines random mutations as those caused by a breakdown in the replication process whereas nonrandom mutations are defined as mutations caused by transposons and genetic recombination. This is not the same type of randomness/nonrandomness that the Modern Synthesis is talking about.
IOW, Shapiro is using personal definitions for these terms.

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Taq
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Posts: 9972
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Message 24 of 760 (609113)
03-16-2011 5:26 PM
Reply to: Message 22 by shadow71
03-16-2011 5:08 PM


Re: Puzzled
When he talks about system architecture and read write memory systems this is not random and is as close to deterministic as you can get without using the word.
What is not random? Chromatin binding? DNA binding complexes? Protein-DNA interactions? DNA methylation? What specifically is not random?

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Taq
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Posts: 9972
Joined: 03-06-2009
Member Rating: 5.6


Message 33 of 760 (609187)
03-17-2011 11:21 AM
Reply to: Message 30 by NoNukes
03-17-2011 1:59 AM


Re: Genetic Engineering
Shapiro's paper is way over my head. But Shapiro seems to be saying that some mutations are triggered by environmental stresses and that these particular stresses produce mutations that are more likely than mere random mutation to be responsive to the stress. Table I of the pair gives a list of stimuli and response mechanisms for various organism along with pointers to substantiating papers.
While I don't see the connection to special creation, since even the presence of "genetic engineering" systems in a cell is attributed to evolution, I also don't see how Shapiro is simply misusing the term nonrandom.
This goes back to the lottery analogy I used in the other thread. The numbered ping pong balls used for the lottery results do not randomly fall out of the sky, nor are they the product of a breakdown at the ping pong factory. The ping pong balls are drawn in a set way on a set day at a set time. In this respect, the lottery is nonrandom in the "Shapiro" sense. There are engineered lottery systems that produce the results. However, the results of the lottery are random with respect to the tickets that were bought. Each and every ticket has the same chance of winning. In this respect, the lottery is random.
How does this relate to mutations? The cell can purposely increase it's mutation rate using specific systems whose purpose is to produce mutations. This is done at specific times in response to specific stimuli. This is analogous to the timing and choosing of the ping pong balls in the lottery. However, like the randomness of the ping pong balls with respect to the tickets the mutations produced by these processes are random with respect to fitness in accordance with the Modern Synthesis.
When molecular biologists talk about random mutations they mean random with respect to fitness. They do not mean that mutations are random with respect to genomic features, time, or environment. Shapiro mixes all of this up. When Shapiro says that mutations are nonrandom he is not referring to fitness. He is referring to genomic features, time, and environment. While all of this can be ferreted out by reading his papers it can still be unnecessarily confusing as shadow has illustrated so well.

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Taq
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Posts: 9972
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Member Rating: 5.6


Message 49 of 760 (609318)
03-18-2011 11:07 AM
Reply to: Message 34 by shadow71
03-17-2011 2:40 PM


Re: Puzzled
Shapiro seem to be very specific in his choice of words and is a highly regarded professional. When he uses the phrase "going from random accidents to regulated biochemical systems" and "heuristic guidance", which to me means they may be discovering or learning something for themselves., leads me to the conclusion that the whole process is nonrandom.
Objection your honor: speculation.
You are misreading what Shapiro says, and then leaping to unsupported conclusions from there. Not a good way to go.
He replied;
quote:
Yes, such as when they activate mobile elements in response to DNA damage, starvation or interspecific hybridization.
So I am of the opinion that he is proposing a system of decision making in the cells that go beyond nonrandom mutation.
If you will remember back in that thread, I actually demonstrated that the mutations produced by these specific mechanisms are random with respect to fitness. I can go over the E. coli DinB mutagenesis process again if you like.

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Taq
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Posts: 9972
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Message 50 of 760 (609319)
03-18-2011 11:13 AM
Reply to: Message 46 by shadow71
03-18-2011 9:37 AM


Re: Modification or replacement
What I am saying is that the chemical/mechanical functions are known, but how and why the information, that Shapiro calls natural genetic engineering, works to have the cell perform those functions is where the new, modified, replaced theory will be discovered.
This would fall under the Details heading that I talked about in a previous post. Shapiro has pointed to specific mechanisms that produce random mutations which helps us better understand divergence between species. For example, when comparing different mammalian lineages we can find explosions in transposon insertions in certain lineages which may have played an important role in the evolution of those lineages. At the same time, these transposons inserted randomly into the genome and were either selected against, for, or were fixed through neutral drift. Again, everything comes back to the basic fundamentals of the Modern Synthesis. What changes is the details.

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Taq
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Posts: 9972
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Message 51 of 760 (609320)
03-18-2011 11:20 AM
Reply to: Message 43 by Robert Byers
03-18-2011 12:49 AM


The only thing I can contribute to talk of genetics and evolution is that genetics is not a trail.
Since creationism sees a great blueprint or computer program for biology then it follows that there is simply a dna score for parts and processes in biology.
for example I discovered marsupials are just placentals with some late adaptations. yet evolutionists try to say marsupials are a group from some ancestor and unrelated to placentals. They invoke the dna formations as showing the marsupials have like dna but unlike placentals.
Well then this demonstrates that the dna was simply a atomic manifestation of the biological change from placental to marsupial.
In short all these creatures got the same dna score because they had the same thing happen to them.
Like body change equals like dna change and addition.
So drawing conclusions of biological relationships from genetics is a waste of time except in minor cases of very close and obvious relationship.
Genetics is not evidence for evolution but it has only been a line of reasoning.
Every single thing you claim in this post is wrong. Just flat wrong. It reminds me of one of my nephews who could never put his shirt on correctly or put his shoes on the right feet. You would think that just by chance alone he would get one of these right 50% of the time, but he never seemed to. You are the same way.
Marsupials and placentals share a common ancestor. They are not unrelated.

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Taq
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Posts: 9972
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Message 73 of 760 (609534)
03-21-2011 11:03 AM
Reply to: Message 60 by shadow71
03-20-2011 2:08 PM


Re: Puzzled
Not speculation, but inferences from what the expert states and clearly admissible.
Objection your honor: hearsay.
If the prosecution has the evidence the court begs them to present it instead of this unending barrage of second hand testimony.
Remember Shapiro said I understood him pretty well, and he is the one who can comment on that w/o rebuttal.
It is time to present the evidence instead of your interpertation of another man's opinion.
But that process does not state what caused the mutations and cannot rule out randomness w/respect to fitness.
The mutations were observed to be random with respect to fitness. Mutations conferring antibiotic resistance occurred in the absence of antibiotics, as one example. Mutations which produced lac+ colonies were not induced to produce these mutations by the presence of lactose.

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Taq
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Posts: 9972
Joined: 03-06-2009
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Message 74 of 760 (609537)
03-21-2011 11:06 AM
Reply to: Message 65 by shadow71
03-20-2011 5:23 PM


Here is a paper by Barbara Wright
That is a review paper. It does not contain original research. We want to see the real experiments and real results from the primary source.

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Taq
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Posts: 9972
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Message 75 of 760 (609539)
03-21-2011 11:08 AM
Reply to: Message 70 by techristian
03-21-2011 12:42 AM


So much true science is being covered up to protect the sacred cow of Darwinism.
You would think that such accusations would be followed by actual science that has been ignored that ties into this thread somehow. It seems that you are big on claims and short on evidence.
There are nearly as many scientists on both sides of the argument and recent finds in RNA and DNA disprove Darwinism.
I look forward to you starting a thread and demonstrating this.

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Taq
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Posts: 9972
Joined: 03-06-2009
Member Rating: 5.6


Message 78 of 760 (609559)
03-21-2011 12:46 PM
Reply to: Message 77 by shadow71
03-21-2011 12:36 PM


Re: Modification or replacement
Shapiro's Natural Genetic engineering is an information based system, where the cells in a regulatory, cognitive manner cause alterations to happen in a single generation and may effect multiple cells and organisms at the same time. These are fundamentally different from the small random variations of the modern synthesis.
This is a perfect example of the mistake you consistently have made in these discussions. Those alterations are random with respect to fitness. The fact that the rate of random mutation is increased by environmental stimuli does not make them non-random as it is described in the Modern Synthesis.
Using a specific example, when E. coli sense DNA breakage due to stress they upregulate the DinB gene. This is an error prone polymerase IV enzyme. What results is an increase in the random mutation rate. All genes are mutated in one bacterium or another. No gene is targetted for mutation, and no environmental cues are used to decide which genes to mutate. The mutations that are produced are beneficial, neutral, and detrimental. All of these types of mutations are produced by the DinB gene product.
The molecular discoveries since the modern synthesis have shown complexity such as seen in the workings of a computer.
Science has also used genetic algorithms based on random mutation and selection to design computer circuits.
Shapiro in an e-mail reply to me also cited on this board stated that the cells are sentient, by which he means they are capable of making decisions that affect their evolution.
The decision that they make is to increase their random mutation rate.
All of this to me leads to the conclusion that evolution is not random mutations for fitness, . . .
All of what? You have yet to present any evidence, only opinion.
Edited by Taq, : No reason given.

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 Message 94 by shadow71, posted 03-21-2011 4:41 PM Taq has replied

Taq
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Posts: 9972
Joined: 03-06-2009
Member Rating: 5.6


Message 79 of 760 (609560)
03-21-2011 12:54 PM
Reply to: Message 76 by NoNukes
03-21-2011 12:19 PM


Re: Conspiracy
Yeah, that's it expunged!
and . . .
Yes, expelled!
These type of arguments always crack me up. It's as if creationists are digging through the trashcans at universities and research laboratories and uncovering all of this data that scientists are throwing out. If only this were true. It would make these discussions much more interesting. Sadly, most creationists have never even read a scientific peer reviewed journal. Perhaps 1% of online creationists have done a single search on Pubmed in my estimation.

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Taq
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Posts: 9972
Joined: 03-06-2009
Member Rating: 5.6


Message 90 of 760 (609600)
03-21-2011 3:47 PM
Reply to: Message 87 by Granny Magda
03-21-2011 3:26 PM


Re: Eh?
I certainly don't think that he is using the word in the way that most people would understand it.
I also think he does this on purpose. He is trying to sell his ideas, so he makes them sound controversial when in fact they are not.
If we accept Shapiro's usage, then a mere assemblage of genetic regulatory systems are sentient.
Indeed. It would seem that even the lowly E. coli has a soul.

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