Natural genetic engineering

 
eudemonia
 
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eudemonia
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17 December 2012 17:34
 

as part of the normal life cycle-this from James a Shapiro and his book about Evolution in the 21st century.

“A major assertion of many traditional thinkers about evolution and mutation is that living cells cannot make specific, adaptive use of their natural genetic engineering capacities. They make this assertion to protect their view of evolution as the product of random, undirected genome changes. But their position is philosophical, not scientific, nor is it based on empirical observations. This section demonstrates that in a large number of documented cases, natural genetic engineering capabilities have been utilized as part of the normal organism life cycle. In many of these cases, utilization involves the integration of different natural genetic engineering processes into a highly targeted and well-regulated series of changes with a clear adaptive benefit. The operation of a tightly regulated sequence of natural genetic engineering events in the adaptive immune system is probably the most elaborate example we have of purposeful genome manipulations. If, as you will see in this section, cells can integrate processes of genome restructuring to serve adaptive needs in normal life cycles, there is no scientific basis on which to argue that cells cannot also use those same functional capabilities to produce significant evolutionary novelties”

Do you understand the implications here? This commentary from Shapiro almost sounds like he is accusing those supporting mainstream accepted science as conspiracy theorists.

If there is so much evidence to support this view, that cells are sentient, make conscious choices, and form adaptations for the good of the organism and nothing is left to ‘randomness’, then why aren’t thousands of biochemists and biologists saying this as well?

This would be, or perhaps will be a huge paradigm shift, and the Darwinian-Mendelian composition of adaptation through random genetic mutation over deep time, is wrong. The neo-Darwinian modern synthesis will be overturned.

And, IMO this theory plays right into the hands of ID’ers who will say it is God (or some supernatural undetectable entity) who gives the cells their power of reason.

 
 
Jezuz_Alrighty
 
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Jezuz_Alrighty
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17 December 2012 18:09
 

If it pans out, secular science will be all over it. If ID’ers want to claim it as some kind of proof, that’s their right. Either way, it will have been led by the work of Darwin, and people who pushed aside all the roadblocks, theist’s, interject along the way. Science flows downhill, to the truth, no matter where it leads.

 
 
Saul
 
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Saul
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18 December 2012 09:48
 

It would only say the Darwinian-Mendelian system is wrong to the extent that Newton’s theories and laws are wrong with respect to relativity. We still use Newton’s laws all the time in calculating ballistic motion and in many other instances, just as we would still rely on, accept and use the Darwinian ideas of natural selection.
Epaminondas I can’t see anything in your post to suggest cells are ‘sentient.’ The so called “highly targeted and well-regulated series of changes with a clear adaptive benefit” could be achieved by complex corrective mechanisms within a cell (which themselves could potentially have evolved) and require no sentience whatsoever. One can easily posit mechanisms which prevent detrimental adaptations from occurring in such a system.
There’s no point worrying about ID’ers either. There is more than enough evidence to squash their claims completely within the scientific community, it just hasn’t because individuals choose to ignore it. A problem which will remain regardless of what new evidence is presented in favor of either side.

 
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18 December 2012 23:45
 
Epaminondas - 17 December 2012 04:34 PM

as part of the normal life cycle-this from James a Shapiro and his book about Evolution in the 21st century.

“A major assertion of many traditional thinkers about evolution and mutation is that living cells cannot make specific, adaptive use of their natural genetic engineering capacities. They make this assertion to protect their view of evolution as the product of random, undirected genome changes. But their position is philosophical, not scientific, nor is it based on empirical observations. This section demonstrates that in a large number of documented cases, natural genetic engineering capabilities have been utilized as part of the normal organism life cycle. In many of these cases, utilization involves the integration of different natural genetic engineering processes into a highly targeted and well-regulated series of changes with a clear adaptive benefit. The operation of a tightly regulated sequence of natural genetic engineering events in the adaptive immune system is probably the most elaborate example we have of purposeful genome manipulations. If, as you will see in this section, cells can integrate processes of genome restructuring to serve adaptive needs in normal life cycles, there is no scientific basis on which to argue that cells cannot also use those same functional capabilities to produce significant evolutionary novelties”

And, IMO this theory plays right into the hands of ID’ers who will say it is God (or some supernatural undetectable entity) who gives the cells their power of reason.

If I understand this, Shapiro is saying that some cells can change their function, depending on what is needed.  There are mechanisms for cutting and splicing DNA to respond to new pathogens. 

This article describes it (written by Shapiro).

A key passage is:
If the cells of the immune system can use well-defined natural genetic engineering processes to make change when change is needed, there is a scientific basis for saying that germ-line cells might do the same in the course of evolution.

I’d say this last quote is quite a stretch.  The immune cells are responding to contact with antigens.  This is very different from egg/sperm cells mutating in response to a perceived need for, say, increased brain size or dexterity.  The connection of the germ cell to the mutated trait is much more remote and intangible than the immune response.

 
hannahtoo
 
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18 December 2012 23:56
 

OK, I just read more from Wikipedia:

This myriad of receptors are produced through a process known as clonal selection.[1][2] According to the clonal selection theory, at birth, an animal will randomly generate a vast diversity of lymphocytes (each bearing a unique antigen receptor) from information encoded in a small family of genes. In order to generate each unique antigen receptor, these genes will have undergone a process called V(D)J recombination, or combinatorial diversification, in which one gene segment recombines with other gene segments to form a single unique gene. It is this assembly process that generates the enormous diversity of receptors and antibodies, before the body ever encounters antigens, and enables the immune system to respond to an almost unlimited diversity of antigens.[1] Throughout the lifetime of an animal, those lymphocytes that can react against the antigens an animal actually encounters, will be selected for action, directed against anything that expresses that antigen.

So here it is proposed that the diversity generated actually precedes contact with the antigen.  It is not cells deciding to mount a suitable response at the moment.  So the Wiki article seems in contradiction with Shapiro.  I wonder who is accurate?

 
eucaryote
 
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19 December 2012 01:56
 
Epaminondas - 17 December 2012 04:34 PM

as part of the normal life cycle-this from James a Shapiro and his book about Evolution in the 21st century.

“A major assertion of many traditional thinkers about evolution and mutation is that living cells cannot make specific, adaptive use of their natural genetic engineering capacities. They make this assertion to protect their view of evolution as the product of random, undirected genome changes. But their position is philosophical, not scientific, nor is it based on empirical observations. This section demonstrates that in a large number of documented cases, natural genetic engineering capabilities have been utilized as part of the normal organism life cycle. In many of these cases, utilization involves the integration of different natural genetic engineering processes into a highly targeted and well-regulated series of changes with a clear adaptive benefit. The operation of a tightly regulated sequence of natural genetic engineering events in the adaptive immune system is probably the most elaborate example we have of purposeful genome manipulations. If, as you will see in this section, cells can integrate processes of genome restructuring to serve adaptive needs in normal life cycles, there is no scientific basis on which to argue that cells cannot also use those same functional capabilities to produce significant evolutionary novelties”

Do you understand the implications here? This commentary from Shapiro almost sounds like he is accusing those supporting mainstream accepted science as conspiracy theorists.

If there is so much evidence to support this view, that cells are sentient, make conscious choices, and form adaptations for the good of the organism and nothing is left to ‘randomness’, then why aren’t thousands of biochemists and biologists saying this as well?

This would be, or perhaps will be a huge paradigm shift, and the Darwinian-Mendelian composition of adaptation through random genetic mutation over deep time, is wrong. The neo-Darwinian modern synthesis will be overturned.

And, IMO this theory plays right into the hands of ID’ers who will say it is God (or some supernatural undetectable entity) who gives the cells their power of reason.

You might check out what Jerry Coyne has to say about Shapiro. In a nutshell, Shapiro describes means of genetic transmission and change other than inheritance, genetic drift, and mutation. He includes means such as “horizontal gene transfer”. Coyne correctly points out, (I think), that though these events can be shown to occur, only blind natural selection can sort them out and select for useful functions and against useless ones. Shapiro’s idea of “natural design” fails.

See Coyne on Shapiro

 
 
eudemonia
 
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19 December 2012 17:12
 

Yes euc, but Shapiro’s point is that it is not ‘blind’ work at all, but naturally designed work, by cells that have purpose.  They seem to ‘choose’ what mutations are required for the proper adaptation of the organism.

Coyne is one of the mainstream thinkers that Shapiro is talking about.

I have not finished Shapiro’s book yet, so I will and give it due process, but I can tell you that Shapiro does not doubt natural selection, he just thinks, and provides evidence, that it is not random or blind at all.

Isn’t it strange how first rate evolutionary biologists can both look through the same microscope at the interworkings within a living cell, but interpret what is going on in there very differently?

Obviously this is a complex and difficult endeavor.

Or, somebody is closed minded or maybe full of flapdoodle.

 
 
eucaryote
 
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19 December 2012 21:55
 
Epaminondas - 19 December 2012 04:12 PM

Yes euc, but Shapiro’s point is that it is not ‘blind’ work at all, but naturally designed work, by cells that have purpose.  They seem to ‘choose’ what mutations are required for the proper adaptation of the organism.

Shapiro is is talking “intelligent design”, pure and simple. There is no such thing as “choosing” or “proper”.

Mutations that survive in the genome do so because they provide functions which provide for adaptation to the environment. The environment does the choosing. The results of mutations, genetic drift or even horizontal gene transfer are still acted on by natural selection. Functional changes are preserved and non-functional ones are eliminated or left in the genome as junk code.

Epaminondas - 19 December 2012 04:12 PM

Coyne is one of the mainstream thinkers that Shapiro is talking about.

Sure, all the ID’ers are down on the “mainstream” evolutionary scientists.

Epaminondas - 19 December 2012 04:12 PM

I have not finished Shapiro’s book yet, so I will and give it due process, but I can tell you that Shapiro does not doubt natural selection, he just thinks, and provides evidence, that it is not random or blind at all.

From his pieces in the PuffHo, it doesn’t appear that Shapiro understands natural selection. As Coyne points out, the evidence he provides is of some genetic changes that may occur by means other than recombination through genetic inheritance, genetic drift, and mutation. Such means may include even horizontal gene exchange between bacterial species.
None of his “evidence” indicates that anything other than natural selection acts to preserve these changes in the genome. Shapiro seems so convinced that he’s onto something new that he’s blind to this obvious fact. There’s no pre-dispositonal or intentional “design” taking place. Just good old blind natural selection that preserves what works over what doesn’t.

Epaminondas - 19 December 2012 04:12 PM

Isn’t it strange how first rate evolutionary biologists can both look through the same microscope at the interworkings within a living cell, but interpret what is going on in there very differently?

Obviously this is a complex and difficult endeavor.

Or, somebody is closed minded or maybe full of flapdoodle.

Extraordinary claims require extraordinary evidence. There are reasons that the “mainstream” evolutionary biologists like Coyne don’t make extraordinary claims. They are scientists and not woo-meisters. Shapiro’s invention of new phrases like “natural design” are very telling of his real agenda.

We have to realize that ALL “design” is the product of natural selection.  Human designers and engineers like myself, serve very much as the tools of a selection process that we have no control over. We carve away that which doesn’t work from that which does but in that sense we are just part of the selective environment. We don’t really get to “choose” what works, we discover what works and then pretend to ourselves that we dreamed it up in advance somehow.

 
 
eucaryote
 
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19 December 2012 22:28
 
Hannah2 - 18 December 2012 10:56 PM

OK, I just read more from Wikipedia:

This myriad of receptors are produced through a process known as clonal selection.[1][2] According to the clonal selection theory, at birth, an animal will randomly generate a vast diversity of lymphocytes (each bearing a unique antigen receptor) from information encoded in a small family of genes. In order to generate each unique antigen receptor, these genes will have undergone a process called V(D)J recombination, or combinatorial diversification, in which one gene segment recombines with other gene segments to form a single unique gene. It is this assembly process that generates the enormous diversity of receptors and antibodies, before the body ever encounters antigens, and enables the immune system to respond to an almost unlimited diversity of antigens.[1] Throughout the lifetime of an animal, those lymphocytes that can react against the antigens an animal actually encounters, will be selected for action, directed against anything that expresses that antigen.

So here it is proposed that the diversity generated actually precedes contact with the antigen.  It is not cells deciding to mount a suitable response at the moment.  So the Wiki article seems in contradiction with Shapiro.  I wonder who is accurate?

Yes, this makes sense. It’s the antigens from the environment that “do the selecting”. The diversity of receptors and antibodies that are created likely arises from from past experience of the genome with that particular configuration. The reason the organism can manufacture such an antibody to recognize a given antigen is due to the experience with that antigen in the genetic past. That antibody configuration has been successfully selected for over generations.

 
 
Larry Olson
 
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21 December 2012 02:46
 
Epaminondas - 19 December 2012 04:12 PM

I have not finished Shapiro’s book yet, so I will and give it due process, but I can tell you that Shapiro does not doubt natural selection, he just thinks, and provides evidence, that it is not random or blind at all.

Even Richard Dawkins thinks it’s not random… for example there is a good reason why we have eye sight.. it’s not random… it’s because people with eyes are able to run away from predators. I wouldn’t call this random, I’d call it the environment shaping or designing us.  This doesn’t mean there is a God shaping us for a purpose.  It just means our environment shapes/designs/modifies us.  If it is sunny outside, people with black skin take the sun better, and more black people replicate since the environment is choosing black skin to block sunlight….  is this random? not random, it’s actually the environment assisting in the design of the final skin color.  This isn’t meant to be a racist post, I’m showing that black skin is superior in certain environments - and it is not random - it’s just a fact.

Our environmental purpose is to not get eaten by predators, and to spread more of our DNA. None of this requires a God, and it’s not random just because there is no God guiding it. If the environment is guiding us, such as lots of sunlight causing people to get more black skin, this is an environment forcing us to change a certain way which is not random at all.  If it was random, then black skin wouldn’t succeed in africa where there is lots of sunlight.. all sorts of random skin colors would succeed randomly. 

The environment does not randomly allow things to survive.. it’s very picky in what it allows to survive.  Some of what makes up a part of evolution is random, but I’ve even heard Richard Dawkins deny that evolution is “Random”. That’s a misconception of the large theory that evolution is.

Now this may boil down to Laynes Law.. a definition of words. What do you mean exactly by random and blind… because even experts in evolution think that evolution is not random or blind.. that’s a common misconception of the grand theory. indeed little sections of the grand theory include the word “random”, such as “random mutation”, but that doesn’t mean evolution as a whole is random entirely, nor is it blind. Maybe call it trial and error… and you can prove that it goes through trial and error. How many species are extinct? Lots. That’s because of trial and error. Some species failed, and others succeeded.. proving there is no perfect design or God behind it all.  A poor designer uses trial and error… a master designer uses perfect mathematics to construct his world.

[ Edited: 21 December 2012 02:57 by Larry Olson]
 
eudemonia
 
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27 December 2012 22:27
 

Yes Larry, I misspoke there. The blind watchmaker is evolution in totality, not natural selection specifically. Natural selection is the part of the process that is NOT stochastic. The neo-darwinists say that genetic mutation is.

Having now finished Shapiro’s book, it sounds and seems to me that he is either some type of ID’er or just a very smart and experienced Scientist trying for a paradigm shift that really isn’t there.

He speaks a lot of very complex words and terms and he has some really cool ideas, but….no real evidence to support his claims.

 
 
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02 January 2013 18:27
 
Epaminondas - 27 December 2012 09:27 PM

Natural selection is the part of the process that is NOT stochastic. The neo-darwinists say that genetic mutation is.

Yes, that’s how I understand it. That a non-random process, (selection by the environment), selects from a menu made of of random changes, i.e. genetic mutation, genetic drift etc. These all in inherited genes. Shapiro wants to add horizontal gene transfer to the list which may be less random but is still subject to natural selection. HGT of “information” that affects the hosts breeding chances will be eliminated or disabled.

Epaminondas - 27 December 2012 09:27 PM

Having now finished Shapiro’s book, it sounds and seems to me that he is either some type of ID’er or just a very smart and experienced Scientist trying for a paradigm shift that really isn’t there.

He speaks a lot of very complex words and terms and he has some really cool ideas, but….no real evidence to support his claims.

Yes, Shapiro is an odd breed as believer types go. It’s why evolutionary scientists like Coyne have such difficulty with them. They have an agenda that is hidden from lay people or less discerning types. Slipping god into science and covering it up with bullshit, (very complex words and terms) seems to be on that agenda.

Thanks for checking back with us Ep.