Does the Darwinian theory require modification or replacement?

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.

The History of evolution began with Darwin and his theory of descent with modification, the origins of hereditary variation or random mutations, and natural selection.

Darwin’s theory was based upon gradual change and positive natural selection.

Next came the Neo-Darwinism or the Modern Synthesis in the 20th century which basically combined Darwinian gradualism with genetics. Again the theory was basically random mutation and natural selection.

Both of these theories rely on mechanical forces, Physical and Chemical, and reductionism.

In a post in the Forum “Biological Evolution” I introduced James A. Shapiro’s 21 st Century Natural Genetic Engineering writings in the “potential falsifications of the theory of evolution”thread.
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Shapiro’s work is based upon discoveries from genome sequencing such as genome alterations in key places in evolutionary history, horizontal transfers of DNA segments, Whole Genome Doublings etc.

He states that the cellular information in the genome is a Read-Write memory system, which is different from the modern synthesis view of the genome as a Read only memory system subject only to accidental change.

Shapiro is of the opinion that Mobile DNA movements rather than replication errors serve as the primary engines of protein evolution.

He writes at page 8 of the above cited paper; One of the traditional objections to Darwinian gradualism has been that it is too slow and indeterminate a process to account for natural adaptations, even allowing for long periods of random mutation and selection. A successful random walk through the virtually infinite dimensions of possible genome configurations simply has too low a probability of success [155] . Is there a more efficient way for cells to search 'genome space' and increase their probability of hitting upon useful new DNA structures? There is, and the underlying molecular mechanisms utilize the demonstrated capabilities of mobile DNA and other natural genetic engineering systems

At page 9 he writes; The second major aspect of evolutionary change by natural genetic engineering is that it generally takes place after an activating event which produces what McClintock called a 'genome shock' [160] . Activating events include loss of food [18] , infection and interspecific hybridization (Tables 3 and 4) - just the events that we can infer from the geological and genomic records have happened repeatedly. Episodic activation of natural genetic engineering functions means that alterations to the genome occur in bursts rather than as independent events. Thus, novel adaptations that require changes at multiple locations in the genome can arise within a single generation and can produce progeny expressing all the changes at once. There is no requirement, as in conventional theory, that each individual change be beneficial by itself. The episodic occurrence of natural genetic engineering bursts also makes it very easy to understand the punctuated pattern of the geological record [161] . Moreover, the nature of activating challenges provides a comprehensible link to periodic disruptions in earth history. Geological upheavals that perturb an existing ecology are likely to lead to starvation, alteration of host-parasite relationships and unusual mating events between individuals from depleted populations.

Shapiro is not alone in advocating a change in evolutionary theory from the modern synthesis as now expressed, to one of Natural Genetic Engineering.

My purpose in this post is to discuss whether the Modern synthesis as it is know today should be modified? Replaced? With A theory based upon adaptations that are directed, modified, regulated and controlled by information exchanges in the cell rather than by mechanical physical, chemical driven adapations driven by random mutations and natural selection.

Thread copied here from the Does the Darwinian theory require modification or replacement? thread in the Proposed New Topics forum.

I really don't see much if any point to the topic.

Looking at science, when sufficient evidence is found to require a modification to a theory and when a mechanism is found that explains the model and mechanism that accounts for the new evidence then theories change.

So far nothing in Shapiro's work seems to require such change or is unexplained. Further he in no way points to any directed non-natural methodology.

Edited by jar, : add an 'h' to wen.

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Anyone so limited that they can only spell a word one way is severely handicapped!

This would be simple to test

starve a few mice for say 10 generations ad compare how much modification happened to their dna compared to the control group that has been fed for their 10 generations.

And eliminate any from of selection by randomly and artificialy breading the population of mice.

my guess the number of mutations from generation 1 to generation 10 in both the tes mice and the control mice would bethe same.

frako writes: This would be simple to test starve a few mice for say 10 generations ad compare how much modification happened to their dna compared to the control group that has been fed for their 10 generations. And eliminate any from of selection by randomly and artificialy breading the population of mice. my guess the number of mutations from generation 1 to generation 10 in both the tes mice and the control mice would bethe same.

Try rewording, I have a hard time understanding how you get to ten generations if you starve gen 1?

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Anyone so limited that they can only spell a word one way is severely handicapped!

A theory based upon adaptations that are directed, modified, regulated and controlled by information exchanges in the cell rather than by mechanical physical, chemical driven adapations driven by random mutations and natural selection.

Well, far be it from me to point out the bleedin' obvious, but however you slice these mechanisms they are in fact "mechanical physical, chemical driven adaptations", because everything that happens to the genome, which is a mechanical and physical and chemical thing, is; and they are subject to natural selection because everything that reproduces is.

Try rewording, I have a hard time understanding how you get to ten generations if you starve gen 1?

Not starve out, just starve them giving them just enough food to survive. while the test group gets an abundance of food.

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

To put it as succinctly as possible:

The theory of evolution is genetics.

jar writes;

So far nothing in Shapiro's work seems to require such change or is unexplained. Further he in no way points to any directed non-natural methodology.

Shapiro in a paper "Revisiting the Central Dogma in the 21st century" published in Annals of the New York Academy of Sciences: 1178: 6-28 (2009) (which for some reason my link won't completely copy out on this page), but can be found by googling the paper in pdf form, wrote when discussing the molecular
analysis of fundamental biochemical processes in living cells wrote:

Lesson 4. Genome change arises as a consequence of natural genetic engineering, not from accidents. Replication errors and DNA damage are subject to cell surveillance and correction. When DNA damage correction does produce novel genetic structures, natural genetic engineering functions, such as mutator polymerases and nonhomologous end-joining complexes, are involved. Realizing that DNA change is a biochemical process means that it is subject to regulation like other cellular activities. Thus, we expect to see genome change occurring in response to different stimuli (Table 1) and operating nonrandomly throughout the genome, guided by various types of intermolecular contacts (Table 1 of Ref. 112). These expectations open up new ways of thinking about the role of natural genetic engineering in normal life cycles and the potential for nonrandom processes in evolution.

Although he is careful to use the term natural genetic engineering he does say that genetic changes are not by accident. He also states that we expect to see changes operating nonrandomly...
This appears to me that he is talking about non random changes that are different from the theory as set forth today.

Dr Adequate writes;

Well, far be it from me to point out the bleedin' obvious, but however you slice these mechanisms they are in fact "mechanical physical, chemical driven adaptations", because everything that happens to the genome, which is a mechanical and physical and chemical thing, is; and they are subject to natural selection because everything that reproduces is.

The difference is that these are driven by information in the cell, not by purely mechanical processes.

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.

This is because you effectively touch upon one of the two basic principles. You go from random mutations to none-random.

Edited by slevesque, : No reason given.

It doesn't much matter how it appears to you. Many of us have explained that his use of terms leaves a lot to be desired, but he is still talking about nothing but plain old natural causes.

If and when there is enough evidence for others to take Shapiro seriously, it's possible that the Theory will change again, but never to the extent that Intelligent Design or Special Creation will be more than stuff to laugh about.

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Anyone so limited that they can only spell a word one way is severely handicapped!

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.

Yeah well I perfectly understand that, I was just saying that hypothetically speaking, what shadow71 proposes would entails a drastic revision, not simply 'details'