https://www.the-scientist.com/?articles.view/articleNo/51153/title/Skin--Remembers--Wou...

"Inflammatory Memory
Our body is routinely assaulted by ultraviolet radiation, irritants, and pathogens. Shruti Naik, an immunologist at Rockefeller University, wondered: “Do these stressors have any kind of lasting impact on cells?” Immune cells are known to “remember” infections and inflammatory events so that they can respond faster to future insults, but what about the epithelial stem cells that maintain the skin and promote wound healing?

"Multiple Assaults
Naik and her colleagues induced inflammation in mice by exposing the animals’ skin to chemicals, fungal infection, or mechanical wounding. Then they measured the time it took for the skin to heal after injuring it in the same place a second time. On average, regardless of the type of injury, skin that had been previously inflamed healed about 2.5 times faster than the skin of mice that were wounded for the first time.

"Swift Repair
To uncover the genetic basis for an “inflammatory memory,” the researchers searched for genetic loci in the epithelial stem cells that were maintained in a chromosomally accessible state after the first injury. Multiple regions of chromatin were left “open” for up to 180 days after an assault, allowing rapid transcription of key stress response genes following a second injury.

"Beneath the Skin
Epithelial stem cells are the first nonimmune cells found to have a memory, and the findings point to “a primitive basic response to jazz up the cells quickly and make them heal the wound,” says George Cotsarelis, a dermatologist at the University of Pennsylvania’s Perelman School of Medicine who was not involved in the study. “It changes the way people think about the skin now.'”

Comment: That DNA (chromatin) automatically remained open indicates a logical cellular automaticity for survival, developed in the course of evolution.


> dhw: Nobody said it was. Taking something for granted is not the same as knowing it for a fact! You wrote, concerning the Cambrian: “I assume God stepped in.” You then wrote: “I do not prefer dabbling as the method He used.” Your two statements are contradictory. We bulldog British never let go. Give in.-No they are not: Assumption is not fact. The Cambrian looks like dabbling, but I repeat, I prefer a full pre-programming. My preference proves nothing, so I am stuck with theistic evolution with no knowledge of the method employed.
> 
> dhw: All three hypotheses fit the history of evolution. The fact that you don't believe my hypothesis is irrelevant.-If your cells are smart enough all three hypothesis fit. Your cells can't hunt and peck their way to the future designs. They are too dumb. Your wishing them some reall intelligence is only wishing.


> dhw: Perhaps this is another example of Americans murdering our beautiful English language. “Assume” in British English = to take for granted that something is true. If you assumed that God dabbled in the Cambrian, you could not favour a different explanation. -We may have inherited the language from you guys, but we have improved it in any ways. I fully known the meaning of 'assume', but it is certainly not as strong as 'I know for a fact'
> 
> DAVID: That is exactly where we disagree. If the cells were brilliant enough the same result is probable.
> 
> dhw;Then you agree!-Note the proviso: 'if the cells were brilliant enough'. They are not according to current research.- 
> 
> DAVID: However, present evidence does not take slightly sentient cells with simple reactions to the level required to plan the complexity and coordination of advanced organisms. Your theory requires extreme faith in those cells, and you eschew faith.
> 
> dhw:I have repeated several times that I offer this hypothesis as an alternative, not as a belief. My objection was to your claim that it didn't fit the history, not to the fact that it didn't conform to our current knowledge of the cell's capabilities.-The history of life's designs, as shown in the Natures wonders thread, requires cells much more brilliant than currently shown. It is much more a stretch to accept Dawkins' comment that nature looks designed but isn't than to say, a designer's hand is much more apparent. Your choice assigns design capacity to primarily automatically functional cells. Show me brilliant cells and I will accept your hypothesis.


> dhw: Confusion reigns. Your assumption is that God stepped in to organize the Cambrian (= he dabbled), but you prefer the theory that he preprogrammed all the new organs and species in the first living cells.-I'm not confused. I admitted I don't know. I prefer to favor preplanning, but dabbling is a possibility I cannot rule out.-
> dhw: We have both long since rejected Darwin's random mutations as the mechanism, and agreed that natural selection only selects from what already exists. The subject of this discussion is my hypothesis of the intelligent cell, and your hypotheses of God preprogramming everything from the very start (which you might call theistic evolution) or God dabbling ..... If you are not a Creationist, you are stuck with God preprogramming every single innovation right from the beginning. Is that really what you believe? -That is what I prefer to believe, but I have no proof of either method, and perhaps both approaches were used.
> 
> I have already accepted that area of your scepticism in the sentence you have quoted. But you claimed my hypothesis of the intelligent cell didn't fit the history, and I pointed out that it offered exactly the same explanation of the history.....You may not believe cells are capable of it, but if they were, that would give us the same outcome as your preprogramming or your dabbling hypotheses.-That is exactly where we disagree. If the cells were brilliant enough the same result is probable. However, present evidence does not take slightly sentient cells with simple reactions to the level required to plan the complexity and coordination of advanced organisms. Your theory requires extreme faith in those cells, and you eschew faith.


> dhw: God “stepped in” (as opposed to organisms inheriting kidney plans he'd placed in the first living cells billions of years back) presumably means he grabbed hold of various existing organisms and fiddled around with their cell communities (organs) so that he could turn some of them into kidneys.-I do not prefer dabbling by God as the method He used.-> dhw: In short, you believe in microevolution but not in macroevolution.-I believe we see micoevolution all the time. Macroevolution is totally unexplained by any scientific theory. Darwin's approach is simply: the final products of evolution are here, therefore they were produced by evolution, let's say by natural selection. Circular reasoning. The whole thing is a tautology. -> 
> dhw: I agree that we have to work backwards, and although I understand (and partly share) your scepticism concerning the inventive powers of cellular communities, I do not understand why you say it doesn't fit the history.-I don't think the intelligent cells have the intellectual power to create macroevolution all by themselves, which opinion is based upon my reaction to the work described by Shapiro.

dhw: Further to what I wrote there, the great advantage of this hypothesis is precisely the fact that deliberate invention by communities of intelligent beings would NOT be itty-bitty, except that it might well require experimentation (with many organisms dying). I am using the same argument as you: the explosion can be explained by intelligent design - in this case, though, the intelligence is that of the cells. -Bluntly, cell intelligence is too limited to create the intricate plans required for complicated organs. You theory does not explain the huge gap of the Cambrian Explosion. My theory assumes God stepped in at this point in evolution.- 
> dhw: For cells to be inventive they would need to be “sentient, subjective, cognitive, communicative and intelligent”, all of which qualities our researchers say they have. I have added decision-making to Shapiro's list. -They are exactly as you say but only to a tiny degree of what is needed for complex planning. One cannot make a kidney by hunt and peck. The Cambrian had full-blown kidney function. It implies a full-blown plan. If you are impressed by spiders spinning webs with pH gradients then imagine a number of different gradients in a kidney, all controlled by feedback signals from other organs in the body.
 
> 
> DAVID: [...] That is exactly why I prefer theistic evolution. It fills all the holes and confusion for me, although I don't know how HE did it. And I think He is challenging us to figure it out.
> 
> dhw: You cannot fill “all the holes” by saying “God did it” though you still don't know how! Once you accept the theory of common descent, “how” is the biggest of the evolutionary holes!-But yes I can. It certainly appears we evolved. The fossils are in the right order in the layers of the Earth. Is God trying to fool us in this arrangement? No, I fully believe God guided evolution. He knows how, but He has not explained it. As stated before, I think that is one of the challenges He gave us when He supplied giant brains. Try and figure it out. I covered all this in my first book on the subject. Let's admit we both don't know how it works, only that we can see the results of an evolutionary process. Since we know the age of the universe the story in Genesis doesn't work. We must treat it as an allegory, so we are left with life evolving over 3.6 billion years.-And there is so much we do not know. Why and how multcellularity developed when bactera are so successful. Why and how sex developed, because sex requires limited life times, and bactera live forever in sister cells. Some of this suggests a drive built into evolution to create complexity. We have to work backward from what we know about the evolutionary process, and from my viewpoint your theory has no way of fitting the history we have found. Certainly not the Cambrian gap. Life is too complex to be a result of chance tentative, in-the-dark attempts by a bunch of cells with some intelligence.

dhw: I have emphasized in the same post that “I am interested only in finding a possible explanation for the innovations which have driven evolution from bacteria to humans.” You keep trying to force the issue back to a first cause, but the hypothesis that intelligent cells cooperated to produce innovations does not cover a first cause, any more than Darwin's theory of evolution did.-And I keep telling ou that cells cannot plan such intricacies, unless you can convince me by describing the method the cells use to plan it out. Using the word intelligence over and over agin gets us nowhere except telling me that magically a fuzzy concept of intelligence in cells can produce complex innovation. 
> 
> DAVID: And are you excluding the issue that it is a logically enormous stretch that cells write their own plans and then follow them. Kidney cells cannot tell liver cells what to do so that the two organs coordinate. 
> 
> dhw: I have no more idea than you do how the cells managed to combine to form these new organs. I only know that they did. Margulis, Shapiro and Albrecht-Buehler tell us that cells COMMUNICATE. So yes, they may well tell one another what to do - but not in any language that you or I would understand. All organisms - apparently even plants - use their own forms of communication. They could not survive otherwise.-Everything you say is true. But I cannot conceive of a group of fairly primative cells becoming very complex cells in a kidney from their own planning. Shapiro describes simple changes. What your theory forgets is the Cambrian Explosion: whole organisms with complex organ systems appear from no precursors. Punctuated equiibrium is not explained by your theory. The whale series of phenotypes is worth your reviewing. Each of the forms is a huge jump in changes from the last form. No itty-bitty here, which your 'cells theory' requires.-> 
> dhw: However, regarding various hypotheses as a possibility is a good agnostic position. I do wish you'd also consider possible the hypothesis that your God invented an intelligence that could take its own decisions. (Oops, of course you do - but despite Shapiro & Co. you insist that only humans and to a lesser degree some other animals can do that. The rest are automata.)-It's not just decisions, it is planning and pre-planning, remember! Simple decision -making does not create overall plans unless you are an architect. Oops, you want cells to do complex decision-making, I forgot. I agree that cells can make tiny epigenetic modifications, which is what Shapiro shows. Doesn't fill the fossil gaps, does it. You theory has to cover the whole picture, not whistle in the dark past the huge holes in it as your cells can only take tiny steps. -> 
> ME: How did innovations happen? Maybe intelligent cells cooperated to create them. 
> YOU: If so, where did cells get their intelligence from? 
> ME: No idea.
> ****
> YOU: God made innovations happen.
> ME: How did he do it?
> YOU: No idea.
> 
> dhw: Of course I'm on the picket fence. Up here I don't have to believe in things that you and I have no idea about.-So we grant cells intelligence from 'nowhere' to create very complex biochemical organs, and then we say, since those organs are present and cooperating, some process in evolution must have done it, but chance doesn't work, so lets stop and not conclude anything. It looks like it must all be a miracle. No, you say, that is not right. It infers the supernatural. That is exactly why I prefer theistic evolution. It fills all the holes and confusion for me, although I don't know how HE did it. And I think He is challenging us to figure it out.


> dhw:The alternative I have offered quite explicitly allows for the cell mechanisms to have been designed:
> 
> 4) Cell communities combined their intelligence (which may have been invented by your God) to design the liver and the billions of other innovations, as and when environmental change demanded or allowed them.-I don't see how these two statements fit together. Original cell intelligence or intelligent information that cells use (in your scenario) to cooperate, can only come from design or by chance. All you have said is 'may have been invented by your God', so does that mean you are excluding chance? And are you excluding the issue that it is a logically enormous stretch that cells write their own plans and then follow them. Kidney cells cannot tell liver cells what to do so that the two organs coordinate. 
> 
> dhw: In this discussion I am interested only in finding a possible explanation for the innovations which have driven evolution from bacteria to humans. You quite rightly say you don't know. Nobody knows. We can only advance theories.-The only explanation I see, considering the intricacies of the body, is design.-> dhw: You keep telling me what I keep telling you: that innovations demand perfect cooperation between the different cell communities, but you categorically reject divine preprogramming, divine fiddling and random mutations as the force behind this cooperation.-No, I've previously said, in complete lack of knowledge, preprogramming is a possibility as is dabbling by God. I don't believe RM & NS are capable of doing the job. As a guess, pre-programming seem to fit more with the concept of God as a first mover.-> dhw: So what else could bring it [innovations] about if not the intelligence of the cells themselves? -And I ask again, explain how did the cells self-invent such intelligence.- You anwser is:-> dhw:The theist can then argue that only God could have designed such an inventively, cooperatively intelligent mechanism, and the atheist can argue that it came about by chance.-And you reject chance, making the picket fence your only refuge, on what seems to me to be a binary issue.


> dhw:You have quite rightly emphasized the enormous complexity of our organs. We know that this requires communication and cooperation between cells and cell communities, but you argue that they are not intelligent enough to invent or cooperate to the degree required. ..... here is the choice:
> 
> 1) Your God made plans for the liver and a billion other innovations to be passed down from the first organisms to their zillions of descendants. 
> 2) Your God fiddled around with a few unlivered organisms till he'd delivered the livers, and ditto for the billions of other innovations. 
> 3) Livers and the billions of other innovations accidentally fashioned themselves through random mutations (rejected by both of us).
> 4) Cell communities combined their intelligence (which may have been invented by your God) to design the liver and the billions of other innovations, as and when environmental change demanded or allowed them.
> 5) ??? (you tell me).-None of the above, because simply, I don't know. I only know that groups of cells practice teamwork. In sports among humans teams need a coach to coordinate their individual efforts. -Once again, the humam living body, as the current pinnacle of evolution, is an extremely complex coordinated group of individually complex organs, acting in exquisite harmony with each other, controlled by chemical messages, nervous messages, hormonal messages, and tightly controlled under a variety of feedback loops. That required coordination is so critical, a minor deviation by one organ can often be fatal. These organs are so complex we bright human engineeers cannot duplicate them but must use stumbling substitutes. Even confirmed atheists (Dawkins) admit is looks designed. I cannot accept that it happened by chance, nor can you.-Your very strained alternative, by severely extrapolating the theories of Shapiro and others, is that the cells did it by themselves. I'll ask you, did the cell mechanisms, Shapiro calls genetic engineering, appear by chance or did the cells invent those mechanisms themselves? It all still comes down to chance or design. Sorry no third way.

dhw: “Information-based rather than stochastic” means that the cell's work is based on information and not on randomness, which would be a precondition for purposeful invention! What do you mean by “intelligent information” anyway? What would unintelligent information be? The cell obviously uses information intelligently.-The cell uses the information properly because it is told to do so. -> 
 
> dhw:There is no “sneaking up”. The cell communities clearly cooperate, and in order to do so, they use their cognitive faculties to exchange information. Of course they have to work together from the beginning. That is what we mean by cooperation! -My response to you is to ask how do cells cooperate to produce a new species? You have no answer and neither do I. Remember that all the info we currently have is that DNA codes for proteins, and they can be modified. We can isolate genes and relate them to certain processes, but we don't know how that gene guidance of processes really works. We do not know how the phenotype of a human being comes out of the DNA, or the phenotype of any other organism. 
An analogy: wwe see a pile of lumber, stones, wires and pipes. Time passes and we see a house. Another pile, another different house. What happened. Workers built the houses accordilng to plans. At this point in scientific research we cannot see the plans, only the results. We do not know how organisms are planned! Our cells are workmen, following assigned duties. Your theory wants them to invent the plans de novo and then follow the plans to a new form. What I am sticking with is that there is need for the desgning architect, who has somehow inserted a planning code into the genome we haven't discovered as yet, or the architect appears from time to time to offer new plans. One or the other must be true as I think about it. 
You give lip service to the complexity of a living human, but without the training I have had you cannot possibly understand how fine-tuned are all the organs in regard to each other and how exquisitely the cooperation is adjusted. Each organ is at a distance from the others, yet satisfies the others needs. Put yourself in the position of a cooperating intelligent cell (your favorite propsition). How does that cell know, sitting in the liver secreting bile, what a kidney cell needs to know or do for a liver cell? These cells are like the folks who built the houses. They must follow a plan, not invent a highly complex plan a little at a time by some unknown method.-> 
> dhw: [My point]is that we only see the results of the process of innovation, and not the process itself. Therefore we do not know from first-hand observation what innovative potential cells and cell communities have.-We certainly know how cells function and what they are capable of in providing for a living organisms. 
> 
> dhw; To sum up: Shapiro says cells are intelligent, but you do not believe that cells can be intelligent enough to create new organs. The organs are there, and the cells must have cooperated to produce them, or they would not have worked. You do not have an alternative explanation, since you accept that evolution happened. -Shapiro presents his new approach to the genome but never carries his ideas to your extreme. I accept his ideas, as a great advance. I do have an alternate explanation. There is a designer/planner. Cells coooperate with the plans they are given.-> 
> dhw: Of course I don't know how the cellular mechanisms work, but some experts in the field have told us that cells are “sentient, subjective, cognitive, communicative and intelligent.” -So they are, but to a much smaller degree than you are willing to accept.-> dhw: So are humans, but we don't know HOW our intelligence works. Does that mean humans didn't invent the motor car? -Poor retort. We know full well the capabililties of our intelligence even if we do not understand consciousness.-> dhw: Bearing in mind that cells MUST cooperate to produce successful new organs, my proposed solution to the mystery of punctuated equilibrium, including the Cambrian Explosion, is that intelligent cells (origin unknown, but maybe “God did it”) cooperated to invent the organs. If your God did not preprogramme every single innovation and did not intervene to make each one separately, can you find a better explanation?-Again, the cells are workmen following a plan, given by God, all at once or one part at a time.


> dhw: May I therefore take it that you now agree that the cell is sentient, subjective, cognitive, communicative and intelligent? (If not, what exactly do you agree with him about?)-I agree with all but the last word intelligent. The cell uses intelligent information. which is just what he indicates. Again from page 146: 'information-based rather than stochastic'.
> 
> DAVID: [...] It is a giant leap to conclude that this explains or even points a way to explaining punctuated equilibrium. All it does is offer the possibility that somehow epigentics causes speciation. It only results in small changes. -The above repeated for emphasis. He does not carry his findings into making any suggestion like yours. He simply describes what cells can do, and severely reduces the role of RM & NS in his thinking. -> dhw: Evolution can only progress through innovation, and since all life is composed of cells and cellular communities, it stands to reason that all successful innovations have to entail cooperation between the cell communities. -Agreed that the cells must work together in new organs. Creating a kidney which controls acid/base balance, electrolyte levels, waste removal, fluid volumes controls, blood pressure control, etc. requires a knowledge of what conditions the other cells in the body must have to function. It all has to work together from the beginning. I see no way to sneak up on it. -> dhw:.... And so instead of arguing that neither automata nor random mutations could have produced such complexities, we can now argue - far more convincingly if Margulis, Shapiro, Albrecht-Buehler & Co are correct - that intelligent beings, working in collaboration with one another, could and did do it in the time shown by the fossil record.-Same problem. Cells use intelligent information to make tiny adaptations. Whole beings adapt to circumstances of nature, and small eppienetic changes appear. Not the way to fill the gaps in the fossil record, or develop a kidney.
> 
> dhw: It might be pertinent to ask why innovation as such appears to have stopped now. The potential for change has to be there still (as we know from continued adaptation), but for the time being, perhaps the cells have no incentive to invent, or have reached their inventive capacity given current conditions. Perhaps it requires dramatic environmental changes to bring forth dramatic new developments. That is why you focus all the time on apparently automatic activities - the innovations have already taken place, and what we see is the outcome and never the process that led to the outcome.-Whoa! We have been thinking about this issue of evolution for 180+ years. Not enough time to see the process in action, unless you think punc-equil might show us a pop-up new species any time now. We see results but we still really don't know how the process works. You and I have debated vigorously and I don't see an answer hanging around.
> 
> dhw; To sum up: Shapiro says cells are intelligent, but you do not believe that cells can be intelligent enough to create new organs. The organs are there, and the cells must have cooperated to produce them, or they would not have worked. You do not have an alternative explanation, since you accept that evolution happened. -Yes I do. God did it, I just don't know how. Darwin's proposal is based on no knowledge of genetics, no knowledge of cellular biochemistry (cells were blobs of plasma!), and studies of breeding in tiny steps. No wonder it looks so weak. His fears of the fossil gaps and of the Cambrian Explosion have een born out. The gaps won't go away and the Cambrian is more of an explosion than ever. Those animals appeared with cooperating complete organ systems. Your proposal does not tell me how.