In a very complimentary blog entitled "Seeing Past Darwin II: James A. Shapiro," James Barham poses the following question and then chides me gently for not answering it:
But if natural selection cannot explain natural genetic engineering, what can?
On this point, Shapiro is admittedly not as forthcoming as one might like. One can see why his opponents -- Darwinists and intelligent design advocates alike -- become impatient with him here. While he is quite correct to point out the philosophical prejudices of his Darwinist opponents, he nowhere comes to grips with the philosophical problem that he inherits from them -- namely, how can teleology and intelligent agency be understood scientifically?
I think there is both an epistemological confusion and a misplaced expectation in Barham's criticism. It may be informative for me to try to explain how I see things.
Natural genetic engineering, the biochemical capacities cells have for remodeling their genomes, does not need explanation. The reality of cells' ability to restructure their DNA has been documented in a long series of empirical observations detailed in my book, Evolution: A View from the 21st Century, and on my website.
Natural genetic engineering is ubiquitous in cells as we know them. It is the collection of cellular processes that create genome variation, the raw material of evolution. Natural selection is a separate process that works in a purifying way to eliminate misfits after natural genetic engineering has generated hereditary variations that need to be tested for their biological utility. (For more detail, see my HuffPost blog posts "What Is the Key to a Realistic Theory of Evolution?" and "Further Comments on 'What Is the Key to a Realistic Theory of Evolution?'")
Apparently, part of what Barham meant to ask was how natural genetic engineering systems evolved in the first place. That is a deep question on two levels, and on one level we cannot yet answer it.
On the first level we do not know why natural genetic engineering systems are as successful as they have been in generating useful evolutionary novelties in the history of life. As I argued in my book, the combinatorial nature of genetically engineered novelties based on preexisting functional modules is vastly superior to random mutation as a search algorithm for exploring the unlimited expanses of possible genome space. (I will soon have more to say about this in a blog on protein evolution.)
But more is needed to account in detail for some of the major evolutionary leaps. These include events like the appearance of bilaterally symmetric animals and rapid speciation following whole genome duplications in protists, fungi, plants, and vertebrates. This gap in our scientific understanding is why we need to learn more about how cell control circuits operate to enhance the genome search process. That is an item on the agenda for early-21st-century research.
On the second level Barham has implicitly included an origin-of-life question: When in the history of the first cells did natural genetic engineering appear? My own guess is quite early. I think the ability to change the genome is a basic vital function. Change is repeatedly necessary to adapt to a dynamic environment, as the fossil record demonstrates so well. Life is the story of organisms that succeeded in changing in response to periodic evolutionary crises.
I took pains in the book to say that origins-of-life questions are still beyond rigorous scientific investigation. We do not yet understand enough about life as we find it. This gap in understanding includes the issues of agency and teleology so fascinating to Barham:
I have a modest proposal for Professor Shapiro.
To his opponents, the way he invokes "natural genetic engineering" will reek of "vitalism," while he himself sees it as plain, empirically substantiated fact. He could go a long way towards satisfying his opponents by making the following distinction explicit:
"Vitalism" has two very different meanings: Either it can mean that life differs from nonlife in fundamental ways -- without further specification of what the difference consists in, leaving the possibility of scientific inquiry into the nature of the difference open. Or else it can mean the dogmatic assertion that science is in principle powerless to inquire into the difference, and will always remain so.
Shapiro ought to make it clear that he endorses the scientific form of vitalism -- which assumes that science will eventually make headway on the problem of what makes life essentially different from nonlife -- and that he resolutely rejects the anti-scientific form of the doctrine.
I am all for science at the empirical and conceptual level, and I recognize the real issues scientific vitalists attempted to resolve. But I decline Barham's invitation, at least for the time being.
Unfortunately, scientific vitalism, as championed by serious people like Hans Driesch, acquired a bad name in the early 20th century. Reliable observations definitely indicated sensory and control processes at work in embryonic development, wound healing and regeneration following experimental disruption. But the vitalists had no objective way to describe the cellular "home" of these capabilities.
Molecular biology has pointed us toward solutions by uncovering complex arrays of sensory, signaling, and decision-making networks in all living cells. In many cases we can enumerate network components and interactions, although in no case can we be sure the list is complete.
How these immensely sophisticated analog molecular networks operate is still a mystery. We can look to electronic computation systems for models and ideas. But I am not aware of any truly original conceptual understanding of how cell circuits operate that goes beyond the limits of current digital computers, which have neither the flexibility nor robustness of cell networks (let alone the capacity to reproduce).
This gap in understanding may just be an illusion resulting from my own ignorance. I hope James Barham can enlighten me. But I also hope he will grant me the right to remain skeptical until convinced. That is the scientific method, after all.
Is vitalism the concept that life differs from non life? Doesn’t that make most of us, including about 100% of the medical profession, believers in vitalism? Is there another term for it? Is there anyone who can’t see a difference between a corpse and a live body.
Shapiro said; “Apparently, part of what Barham meant to ask was how natural genetic engineering systems evolved in the first place. That is a deep question on two levels, and on one level we cannot yet answer it”
The “yet” might be a little presumptive. Science might eventually make headway on the problem of what makes life essentially different from non-life. Science may or may not someday explain genetic engineering, consciousness, purposeful adaptation, free will and cognition. I’m sceptical that science will eventually explain everything. That’s no reason to declare that anything we don’t understand as nonexistent. The debate is really over religion. The evangelical atheists want an explanation that specifically eliminates any possible intervention by a deity. Random mutation and natural selection, absurd as it is, is the only such explanation anyone has been able to devise. Shapiro's discoveries are exciting. - even if they don't disprove theism.
A Few Autistic Questions about Freud, Marx and Darwin.
Berthajane Vandegrift
"We should not let creationist pressure alter the way we do science — the day that researchers become reticent about highlighting inconsistencies and uncertainty would be a dark one. But equally, we are not helpless when it comes to countering creationist disinformation based on our results. I believe that science would benefit greatly if we did more outreach when we publish and publicize our research."
"Ignoring the creationist threat will not make it go away. As scientists, we owe it to the schoolchildren of Tennessee and elsewhere to find another way to beat it."
Scott Hatfield and I believe you haven't done this sufficiently yet. I hope that with your new-found realization that the Discovery Institute is distorting your work, that you will heed Garwood's advice:
http://www.nature.com/news/reach-out-to-defend-evolution-1.10640
The problems come from both sides. The creationists claim any valid criticism of old-fashioned Darwinism and neo-Darwinism as evidence of supernatural intervention. The neo-Darwinian fundamentalists, like Jerry Coyne, deny that anything is new in evolutionary science (that's what his "garden-variety natural selection" crack was meant to convey).
As I answered to Bill Dembski (on his own turf in spite of the objections you express), I prefer to remain in the DMZ between creationism and Darwinism because that is where the real evolution science is going on. I hope you can one day appreciate why I say that.
Anyway, vitalism probably misstates Shapiro's argument. I think he's trying to point out that random mutations are not the main source of genetic diversity. Instead, cells know what is good for them and strive toward certain traits that they recognize are best for their own survival. If this is true, it will be a revolutionary leap in our understanding of evolution and the process of getting from one animal to another.
Conscious: Aware of and responding to one's surroundings; awake. Having knowledge of something; aware.
Cognition: The mental action or process of acquiring knowledge and understanding through thought, experience, and the senses. A result of this; a perception, sensation, or intuition.
More interesting and possibly or seemingly more pertinent, is connection to neurons giving rise to our somewhat similar conscious experience and biochemical capacities cells have for remodeling their genomes; apart from natural selection. Dynamic accelerated genome remodeling might or likely suggest mutual connection.
Just a guess, of course, but quantum fluctuations underlying all subatomic cell structures would seem likely connection to intangible conscious or cognitive (whichever term preferred) ability via higher energy state surrounding and influencing all biological cells, everywhere. I understand some are comfortable accepting emergent property, but that definition explains nothing.
My guess is the emergent property advocates don't like this sort of idea, because it upsets their dogmatic form of materialism cum "chance" universe-but I think the idea of Life as a self-regulating system is compelling-and it would seem some contemporary scientists are moving in that direction.
Reminds me of Tao-nothing unnatural ot supernatural about it.
For those in the West who are obsessed one way or the other, with the issue of God/no God, check out SPINOZA. No teleology, one substance monism, pan-causality-Einstein liked it. and even Christopher HItchens allowed Spinoza his "God exists, only philosophically"-not as "spontaneous" as Tao, though.
A Few Autistic Questions about Freud, Marx and Darwin
Berthajane Vandegrift
I agree with you, Bertvan. I have disagreements with the Discovery Institute too but they've performed the much needed job of pointing out the Emperor is wearing nothing but a jockstrap.
But I believe most telling of all re: Neo-Darwinian automatons is the torrent of insults, epithets, bullying, ad hominem attacks, name calling and intolerance. In Chicago we've got a group "The Darwin Bulldogs". Funny how Darwin's the only great scientist who needs bulldogs to defend him. Other scientists seem to do OK without zealots.
I mean no insult to Darwin, BTW. Today I read a fascinating paper,
The 'root-brain' hypothesis of Charles and Francis Darwin: Revival after more than 125 years
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2819436/?tool=pubmed
Most folks don't know Darwin theorized that plant roots are brain-like. Botanists then derided him but this paper shows new research supports his idea.
The authors use terms like "Cognition" in much the same way Shapiro does and draw similar conclusions on how we've tended to underestimate the capabilities of living things. It seems Darwin was no Neo-Darwinist. As a result of this paper, my respect for Mr. Darwin went up a few notches.
http://lippard.blogspot.com/2008/04/david-bolinsky-on-expelled-and-dembskis.html
And then Dembski thought he was saving our republic from the threat of potential bioterrorism from eminent University of Texas ecologist Eric Pianka, falsely accusing him to the Federal Department of Homeland Security as a potential bioterrorist:
http://freethoughtblogs.com/singham/2012/04/21/william-dembskis-new-job/
And then there was an incident where Bill Dembski thought he could censor a harsh, but accurate, review I had written of one of his books over at Amazon:
http://scienceavenger.blogspot.com/2007/12/john-kwok-vs-william-dembski.html
Perry, are you sure you still want to stand by your statement re: "Neo-Darwinian automatons"? Bill Dembski is the worst example, but his Discovery Institute colleagues David Klinghoffer, Casey Luskin, Stephen Meyer and Jonathan Wells are nearly as reprehensible.
I agree with you that arguments and statements should be judged on their merits, not on the identities or affiliations of the people who make them. Real intellectual discourse requires mutual respect and honesty from the participants. I objected to misrepresentation of what I actually said.
David thinks that my citing the cognitive abilities of cells and their networks somehow places me outside the materialist framework of science.
I cannot follow his logic. Are cells and their molecular networks not material? Are human beings and other organisms we agree to be cognitive not material?
Does David think that cognitive processes somehow catapult us into the realm of disembodied spirit or the supernatural? That is certainly not where I wish to go. As I try to make clear in my book, I am not a Cartesian dualist. In my view, cognitive/mental and material processes are inextricably linked.
I would be grateful if David would stop implying that my arguments are based in anything other than scientific naturalism.
I assume you address this question to me. I will try to explain these concepts as I understand them from the perspective of a practicing scientist, not as a philosopher or professional epistemologist.
Reductionism is the process of taking a complex entity apart, defining its components, and assigning properties to those parts. This is standard analytical operating procedure in experimental science.
Reductionism may also mean the philosophical approach of explaining the behavior of a complex system from the properties of its component parts. This form of reasoning is common in the physical sciences and is often confused with scientific materialism, even though it is not the only materialist approach possible.
Integrationist approaches which treat an entire system as having properties not deducible from its component parts can also be materialist. A simple example of the integrationist approach is to say that water molecules have properties which cannot be deduced from isolated hydrogen and oxygen molecules.
Materialism is the philosophy of attributing the properties of an entity to its material composition without looking for external inputs of a non-material or spiritual nature. This is where scientific vitalism ran into trouble because it could not provide a material basis for the sensory and regulatory capacities of living organisms.
I would like to know: What scientific fact bars consciousness from investigation and hypothesis? How is this anything other than an externally imposed limitation?
Bonnie Bassler gave a riveting TED talk on how bacteria talk to each other: http://www.ted.com/talks/bonnie_bassler_on_how_bacteria_communicate.html -- they live in colonies, they broadcast and receive molecules that form words; they have both interspecies and intraspecies dialects with sophisticated linguistic structures.
I have no idea what the nature of cellular self awareness is; we can only wildly speculate at this point. What we do know is, they behave very similarly to larger animals and they possess sophisticated signalling systems.
It make Barbara McClintock's question "What do cells know about themselves?" which Shapiro discussed at http://www.huffingtonpost.com/james-a-shapiro/barbara-mcclintock-x-rays_b_1322879.html all the more interesting.
What does my dog know about herself? Or my cat? Or my son's hamster? Or my kids' fish? If it's a valid question for our house pets, why isn't it equally valid for plants and microorganisms?
What would happen if we were to let nature speak for herself, rather than imposing materialistic dogmas on our observations?
"What do cells know about themselves" is a far more fruitful and provocative question than doctrinaire insistence that they can't possibly know anything.
I prefer to use the term "cognition" because I can give it an operational definition, which is action based on knowledge. "Consciousness" brings in a whole host of additional properties which have great emotional meaning for us. Nonetheless, in the final analysis, these terms are merely words, and they are significant to the extent that we can invest them with useful meaning. So, from a scientific perspective, we should use them as guides for making testable hypotheses and empirical observations. If they serve us well in those tasks, then we are using the terms properly.
As usual, you're jumping to unwarranted conclusions. "Instinct" is just as arbitrary and ill-defined a term as "consciousness."
What we know is that bacteria communicate chemically with a wide vocabulary of intra- and inter-specific signals. They sense signals from other cells and adjust their behaviors accordingly. Whether or not this is purely automatic, as you seem to believe, or involves a more sophisticated decision-making process, as Perry and I believe, remains to be thoroughly examined experimentally. However, the number of cellular activities subject to intercellular communication between bacteria continues to expand every year.
You may be interested to read the following papers (available from my web page) before you respond:
Shapiro, J.A. 1988b. Bacteria as multicellular organisms. Scientific American 256 (6), 82-89.
Shapiro, J.A. 1998. Thinking about bacterial populations as multicellular organisms. Ann. Rev. Microbiol. 52, 81-104. http://micro.annualreviews.org/cgi/content/full/52/1/81
Shapiro JA. 2007. Bacteria are small but not stupid: cognition, natural genetic engineering and sociobacteriology. Studies in History and Philosophy of Biological and Biomedical Sciences 38 (2007) 807–819.
I appreciate that John Kwok has been so insistent in pointing out when people are relying on this alternative expertise base. It's a frustrating propaganda war for science, which seems to be losing out to technically much weaker foes but far better marketing, eerily reminiscent of the demise of BetaMax.
Although I am sincerely very sympathetic to some of the concepts James discusses, such as complex cognition in cells and very sophisticated genetic self-correction mechanisms, I find his philosophy of science very foreign. When he says that the phenemona he discusses are documented and real, therefore they need no explanation, he is voicing a sentiment I find utterly alien to the way I think of science, Science to me is fundamentally about how things work and how we explain them, not about making a collection of unexplained observations.
"Vitalism" and "teleology" can be made reasonable subjects of analysis in scientific terms, but only if great care is taken, and there is little if any such care taken by the proponents of Intelligent Design in my experience.
http://www.amazon.com/Creationisms-Trojan-Horse-Intelligent-Design/dp/0195319737/ref=sr_1_1?ie=UTF8&qid=1337254945&sr=8-1
I find Ron Numbers to be a reliable and fair historian of the Intelligent Design movement and its well-meaning motives.
Randall Stephens book "The Anointed" seems to give a good sense of how the larger movement has produced an alternative authority base from a religious perspective as well.
The background history of the alternative tradition of anti-intellectualism in the US is covered particularly well by Richard Hofstadter in his books.
The point is, we don't just readon from evidence, our thinking is shaped by what is consistent with what we already believe and our habits and preferences of thought. Jon Haidt covers this topic particularly well in "The Righteous Mind." Over time and partly deliberately, the tradition of anti-intellectualism has been leveraged into distinct expertise sources from the tradition of intellectual scholarship. To me this is an important historical pattern to be aware of, regardless of where one stands.
Dr. Shapiro,
Soon the rest of the world will learn of these fascinating discoveries and the world will be better for it! What else is fascinating is watching your detractors do everything possible to keep these closely guarded discoveries from ever reaching the general public! That in itself speaks volumes that they cannot refute your discoveries and have no other options except to follow you and troll! They have no clue that their overt display of unprofessional behavior is backfiring on them!
In addition, perhaps they can learn more from you regarding their continued tired argument of "consensus"
"Science advances by argument, not by consensus" - James Shapiro
"Living cells and organisms are cognitive (sentient) entities that act and interact purposefully to ensure survival, growth, and proliferation. They possess corresponding sensory, communcation, information-processing, and decision-making capabilities.(p. 143)"
As far as I am concerned such thinking would be better suited for science fiction like George Lucas' "Star Wars" saga or Frank Herbert's "Dune" than it is for science. Why? Fundamentally this is a theological, not a scientific, argument.
Yes we do - the good ones spread quickly through the population.
http://www.thebestschools.org/bestschoolsblog/2011/11/24/introducing-denyse-oleary/
While it is possible to take something like a seed apart and analyse it into its material constituents, and processes, there is a basic idea of what the thing is that we are analysing and how the various bits and pieces make up this whole. Without this implicit understanding of what we are doing the analysis would end up spiralling off into ever more fundamental analysis. We would loose ourselves and our objects in an infinite regress of analysis. Reductionism tries to do the analysis and then claim to have exhausted its object but it cannot explain how it is that it knows when to stop.
The idea of a living thing being future oriented is implicit in all analysis that keeps a view of its object. It is not necessary for something to be conscious of a possible future to be internally organised toward it. However it is one of the key facts about consciousness that it is objectively evidenced in the degree of foresight discernable in it. Something can be objectively future oriented, or both this, and subjectively oriented as we human beings are. A seed in this sense is an objective inference about a possible future.
I think some of the kinds of processes that you describe can perhaps be seen in this light.
http://www.talkorigins.org/faqs/kansas/kangaroo7.html#p3272
Barham is well known as an Intelligent Design advocate. Moreover, his website includes as a contributor, the notorious Canadian Intelligent Design advocate Denyse O'Leary:
http://www.thebestschools.org/bestschoolsblog/2011/11/24/introducing-denyse-oleary/
For these reasons alone, James Shapiro needs to treat with ample skepticism, Barham's praise for Shapiro's concept of "natural genetic engineering".
He posts this on one of his websites (http://lclane2.net/barham.html):
"ID, it seems to me, most naturally predicts convergences of the sort we encounter in human engineering, based on design requirements under similar constraints---such as the streamlining we find in ariplanes (and birds) and submarines (and fish)."
"What I am saying is that teleology is real, it exists objectively in organisms themselves, and that this means that biological matter is active, not inert."
He has consistently expressed doubt about "Darwinism" for years now, echoing views expressed by his fellow Discovery Institute creationists, and is a regular contributor to its Evolution News & Views website (which Shapiro has contributed to) as noted by Discovery Institute creationist David Klinghoffer:
http://www.evolutionnews.org/2012/05/if_james_shapir059691.html