Refactoring The Human Body

(See SimplicityIsOverRated.)

The human body is way too complex - please refactor! Vast stretches of "junk DNA"; the appendix; copy-and-paste engineering all over the place... Let's make it simpler.

Junk DNA? I thought there were fragments of defeated viruses in junk dna that help us to defend against viruses (by base pairing). Use of introns is still completely speculative.

Okay, off to the labs. Here we have our brand-new model 01. Every piece of DNA has precisely one purpose. Ears have been changed to parabolic dishes. Toes were more complex than was necessary to provide balance, and not terribly useful as manipulators, so we've removed them (sorry, foot fetishists). And, most importantly, the immune system has been made rational.

Wait a minute - if the immune system is rational, doesn't that make it easier for bacteria and viruses to evolve in such a way as to circumvent it? Nature's version was SecurityThroughObscurity or ImmunityDesignPrinciples, depending on your point of view, but since there was no thinking opponent attacking the system, that worked pretty well. (Of course, ever since the protein-folding problem was solved in the year 3200, in theory there could be a thinking opponent - but world peace was obtained in 2500, so there won't be.) Hmmm. Yeah, it probably does make it more vulnerable, but the hope is that the increased order will be so effective that would-be invaders will die completely, with no chance to evolve.

What's irrational about the immune system? The bits I can understand are beautifully elegant. -- TomAnderson

This came in yesterday via the retrotemporal TCP gateway, and I wondered what relevance, if any, it might have to software design. Thoughts? -- DanielKnapp

If it doesn't work, the universe can always start over. It may take a while with only 40 hour work weeks and every mucking with everyone else's product. But maybe nothing will happen as there is no customer? -- AnonymousDonor

If nature can be said to have an intelligence, it's a lot smarter than any human. Nobody can keep all of the knowledge about the human body in his own head. Even with the limited amount that we know today, doctors are beginning to segment into tiny specializations.

As humans, we should respect complexity, but strive for simplicity. The answer is simply one of avoiding hubris; anybody who created a computer system with the complexity of the human body is heading for a fall when he's asked to maintain it later.

Some Arabic master rug-weavers would always embed one small imperfection into their grand carpets. Perfection, it was said, was solely the province of Allah, and for a mortal to attempt perfection was impious.

Wait a minute - if the immune system is rational, doesn't that make it easier for bacteria and viruses to evolve in such a way as to circumvent it?

Because heaven knows they've been having massive amounts of difficulty circumventing what we have now.

If the above comment was meant sarcastically, you only have to look at what happens to immunocompromised people to see just how well the immune system is working now. My guess is that the immune system is fairly well calibrated to minimize both false negatives (missing invaders) and false positives (attacking self).

I'm sorry, but pointing out that conditions could be much worse doesn't mean that they're good now. Your argument is not valid. If it were, then malaria would be a good thing because AIDS is worse, and even AIDS would be a good thing since Ebola is worse. See below for an explanation of how to make ourselves immune to all viruses.

The actual argument above was that it is unlikely that the immune system is being kept "weak" deliberately, but rather than the immune system is as strong as is practically viable without being strong enough to trigger auto-immune disorders such as lupus. The viral "solution" presented below is a naive underestimation of the way in which viruses arise and evolve. Humans can't even control viruses in computer systems designed, maintained, and (hopefully) fully understood by humans so claims of systems for invincibility to biological viruses must also be suspect. In a broader repect, current biological solutions represent adaptation to reasonably probable circumstances, rather than outright invincibility. Efforts to achieve invincibility in other areas of human endeavour have generally failed, suggesting that adaptability may be the best solution available.

Ears have been changed to parabolic dishes.

Is that why post-humans can't locate the origin of sound sources any more? After all, the misshapen human ear deliberately distorts sound so as to provide cues as to its direction of travel.

Well, conceivably if they were better at discerning small differences in volume, sound sources could still be located at least as well as they are now - there are two ears after all. Nice point though.

With parabolic ears where do you plan to put the tympanic membrane? Surely not at the focus of the parabola???

Important question: are we limiting ourselves to flesh? Can we, unfavourably, compare the human body with optical fibers and copper wires? Can we use hypothetical nanotech materials?

Mmmm... sure, why not? I think this is one of those questions that's made more interesting by dropping limits than by adding them. Speculating about improving the *mind*, however, should probably be off-limits on this page at least. -- Dan

Just saw "Alien Resurrection" last night. Hmmmm...

Not to mention Gattaca, Brave New World, and others.

I've always considered the "supermen" of that ilk to be extremely uncreative. "Immune to disease", yeah, that's easy to say...

Trivial to do too. At least immunity to viruses. All you have to do is re-encode all of the DNA using some other DNA-protein encoding and then change the ribosomes and other translation mechanisms to compensate for that. So you get the same proteins from completely different DNA and your DNA-translation mechanism is no longer compatible with any other's on the planet. The result is that viral DNA now only produces junk when translated by your ribosomes.

Cool. Though it would be better if you replaced DNA with something having a different chemical structure (better, but rather more difficult); if you change the encoding, then sometime soon (any society that has mastered this sort of manipulation will probably be made of nigh-immortals, so yes, "soon") new viruses will evolve for the new encoding. If you change the whole structure, then there is no other organism or sub-organism in existence from which viruses could evolve. I'm not certain I buy this my own argument though; something could form which incorporated *NA from dead human-prime skin cells...

Easily taken care of. Every few million years, you re-encode the whole of human DNA using a completely new encoding. And even if viruses incorporated *NA from human-primes, I don't think this would help them any. I think the problem would still be on the same order as constructing a new virus from scratch. It would certainly not be the incremental job which is the only thing evolution is capable of. Since ribosomes et al are one-way functions, there would be nothing in the new DNA which a virus could use to re-encode its own DNA. And ultimately, changing over to PNA is still on the table.

This happens in a GregEgan short story called 'The Moat'; it's in Axiomatic. Axiomatic is a collection of short stories. It should be available from bookshops. ISBN 1-85798-416-1 .

I strongly recommend Axiomatic to every thinking entity in the universe. -- TomAnderson

Basic Refactorings of the human body

Urethra doesn't gratuitously pass through the prostate, leading to infection (evidence?) and prostate cancer (citation?).
Immune system doesn't become super-sensitive when developing in the absence of pathogens. That is, immune system doesn't give us auto-immune diseases like asthma when tuberculosis is not present during development.
Pinkies turned into opposable thumbs. What advantage? So that we can strip bamboo like pandas do?? For whatever advantage robot designers see when they use three separate fingers. (Actually... don't they just do that because programming a full hand would be too complex? Which isn't an issue here; we won't be programming it.)
Nerves in wrists moved into positions which better protect them from the strain of typing. (Or not, since typing is presumably obsolete.)
Retina not connected to nerves at the back of the eye so that the optic nerve doesn't need to go through the retina, leaving a blind spot. But see http://www.catalase.com/retina.htm.
DNA replaced with PNA. (See http://www.highveld.com/pna.html)
Powerful error-correcting codes bring mutations to a halt even in high-radiation zones. So what if this stops evolution? You can't improve on perfection! (A brute force search of possible human designs, evolution, can't possibly compete with an intelligence, given the same computing resources.) (Concur.) Do you also propose total error correction in DNA->RNA->protein translation? If not, why not? The integrity of object factories is more crucial than of object instances.
Ability to synthesize vitamin C. (What, just because some ancestral rat lost it means we depend on citrus fruits?)
Attraction to and storage of fat kept under control. Seems that after millennia of civilization, the human body still hasn't adapted to fat abundance. (Question: do any of the people who believe in the elegance of the human body live in the USA?) Cells should be able to synthesise glucose from acetyl coenzyme A; see below.
No surge of energy and well-being when starving, hence no anorexia! (Wouldn't the surge of energy help survival, when in a real emergency situation? Of course that could be argued either way; conscious control of how the body's resources are used would solve the problem once and for all, but it's not clear whether that falls in the scope of speculation here, since we the speculators have no idea how to do it.) First principle of design: do not fuck up normal everyday situations like self-conscious adolescent girls for highly unusual and unpredictable events. AnorexiaNervosa? is a psychological illness; getting rid of starvation high wouldn't cure it.
Maintenance of muscle-tone even when perfectly sedentary. (Nice trick!) You're asking for a machine to deliberately not optimise itself for the task it does?
Each protein's base-chain refactored so it folds simply and predictably. No need to solve the protein folding problem with rational proteins. And with predictable folding comes the absence of prions and so non-existence of MadCowDisease?. An example of such a protein would be instructive; proteins need complex structures to do their jobs, and it's hard to see how you can get that with 'simple and predictable' folding.
Secretions made during sexual activity should taste like chocolate. Would provide an affordance to separate recreational sex from procreational sex.

On the synthesis of glucose from acetyl coenzyme A. There are basically two types of fuel for the body: sugar-like and fat-like. Sugar-like fuels are broken down to pyruvic acid, which is then converted to acetyl groups (attached to molecules of coenzyme A (CoA)); fat-like fuels are broken down directly to acetyl groups. Cells can reverse the flow from pyruvate to sugar and from acetyl CoA to fat, but cannot make pyruvate from CoA. This sets up an irreversible flow from sugar to fat, which is really awkward in many situations. Plants can do the reverse, and we can almost do it (acetyl CoA to malonic acid (?), which is only a couple of oxygen atoms different).

Evaluation of the human design in light of standard engineering practices and construction materials

nerves that transmit electrochemical signals at 10 m/s tops instead of electrical signals in copper wires travelling over 200,000 km/s. There is also processing en-route. Hardly any processing compared to the slow-down. The slow-down is due to using gooey, non-solid-state, chemical signals.
a big win on maintenance; see below.
dependence on a massive databank of foreign DNA (the gastrointestinal flora.) alternatively we are leveraging the design of the flora. Ever heard of software re-use? You mean leveraging third-party proprietary DNA over which you have no control? Especially the DNA of entities which may have an incentive to kill you?
cancer - is this a design issue? is there a parallel in engineering? It's definitely an issue. People's fears of MolecularNanoTechnology largely stem from the expectation of cancer, mutation and evolution in nanotech. These fears are completely groundless. There are plenty of rational grounds to fear nanotech but the decrepitude of biology so clouds people's minds that they can't address rational fears for the irrational ones. (I'm not convinced that these fears are wholly irrational, though certainly they aren't applicable to anything being developed today. New page would be appropriate for this one, I suspect...)
inability to excrete toxic metals (lead, plutonium) and chemicals (PCBs and other fake hormones) except through breast milk. There's an examplary evolutionary solution for you: detoxify yourself by poisoning your kids! though when it comes to infections it's not such a bad strategy. Infants gain some immunity (e.g. to malaria) through breast milk. The good strategy is to excrete toxins through urine or feces so that it never enters breast milk! The fact that breast milk is still vastly superior to formulae for infants, no matter how contaminated, has no bearing on the fact that contaminating breast milk is sheer idiocy in the first place.
inability to photosynthesize. our lesser surface area is better employed making vitamin D. And the utilization of light impacting the human skin is why we're all a deep green. Black people have dark skin because of melanin, which is an antibacterial agent and not emloyed in the synthesis of vitamin D.
the organization of the mind would be on-topic on ArtificialIntelligence, perhaps. It's on-topic here. The lack of connection between the two hemispheres of the human brain is due to clear physical factors. Unfortunately, psychology, and especially historical psychology which deals with our lunatic ancestors, is very disturbing to most people who aren't ready to deal with the fact that grandpa and grandma were nuts. (Or to those of us who are still dealing with the fact that grandpa and grandma are nuts. Sigh.)
muscles made of "jellied crud re-engineered from bags of seawater" (though using an innovative Brownian motor). show me a better 'muscle' in a man made robot. That's asking a bit much considering we only discovered how to exploit Brownian motion a few years ago.

Regarding maintenance:

The body is self-repairing, unlike anything designed by humans except some NASA satellites. Architectural feats, such as bridges and skyscrapers, last much longer than the body, and require almost no maintenance (repainting exposed structural cables counts, but recarpeting is not maintenance in this sense). Automobiles are highly maintainable (and do need it), but their average driveable life is far less than the human lifespan.

The achievements of our 'planned obsolescence' culture are not indicative of our engineering capabilities. The Romans built highways and aqueducts which still stand today; we could do so much better now. (And in any case, the only self-sufficient lifeform in the industrial sector is, for now, the entirety of industry - and it does a hell of a lot better job at repairing and evolving itself than nature does.)

And what facilities of the human body are proposed as being devoted to maintenance anyways? I see only two. 1) healing of broken bones. 2) scarring. Everything else results from confusing the necessary development of the human body to breeding age with its continued maintenance. The human body is built for planned obsolescence as much as the worst examples of our consumer culture. The fact that every system in the human body breaks down simultaneously after a mere century gives away how much planning nature has put into the destruction of the human body. And 'premature aging' is a dead give-away.

Other examples: regeneration of the liver after resection, blood clotting, continual replacement of skin hair and blood cells. At the molecular level, multiple pathways for maintenance of DNA including base repair, excision repair, mismatch repair, nick repair, double-strand break repair. Protein degradation and replacement. Essentially, anything critical that is likely to break (on an evolutionarily relevant timescale) has a system for repair. -- AndyPierce

Continual replacement of skin cells is necessary for the biological function of skin. This is the only way that nature has come up with to create a relatively disease free protective outer coating.

The same goes for excision, nick and double-strand break repair. These are necessary to the function of DNA replication, which requires cells to unpack DNA from bizarre shapes because of the stupid storing system that gets it all tangled in the first place. And because of this, perhaps mismatch repair belongs to the category of "healing self-inflicted injury".

DNA packing is an example of a well-designed hierarchical storage system!

Consider what's left now. It's all "continual replacement" of this and that. This demonstrates the amount of thought put into maintenance compared to development; none, nada, zilch. "continual replacement" just means you don't bother turning off your production facilities after they've finished their initial run.

Other systems that deserve mention are the nervous and immune systems. The nervous system is absolutely horrible at self-repair and maintenance. Its main self-repair capabilities stop around ages 3, 6 and 9. What's left in way of self-repair is redundancy between the left and right hemispheres.

The other way of looking at this is that engineering does the wrong thing (try to build for eternity by investing a lot of effort up-front) and biology does the right thing (DoTheSimplestThingThatCouldPossiblyWork and then replace it when it wears out).

Ahhh, yes - so that's why the brain replaces nerve cells when they wear out or are damaged in some way.

Either you're being sarcastic, and saying that the brain doesn't do this when it should, in which case your knowledge of brain physiology is out of date, or you aren't, in which case I am afraid I don't understand your point, and would like you to elaborate.

The immune system is about the only maintenance system worth consideration. It's also the most complex in the body after the nervous system. Consider how it would be replaced though were engineers to do the job:

an unbroken protective outer coating (eg, solid state cameras at regular intervals around the head - no eyelids)
a strong skin that doesn't invite pathogens to feed on itself
the immunity to viruses mentioned above
elimination of the gastrointestinal flora
recycling of raw materials, not an endless ingestion-digestion-extretion cycle to which half your internal organs are devoted
impermeable mucus membranes, which have less surface area if we run on gasoline and none if we run on electricity

So if engineers did it, there wouldn't be a need for the immune system.

I suspect that a lack of understanding is limiting your ability to fully appreciate the elegance of current biological systems, nevertheless, I look forward to observing how well your engineering solution performs in the field.

It's just BiologyEnvy?.

That's ridiculous. If anything, I have EngineeringEnvy.

So if the question is one of human engineering prowess, let's ask this: What currently existing human technological invention satisfies as many requirements as the human body, and needs the same or less maintenance?

If that's too hard, then perhaps we could see some concrete designs for improvements? It's easy to say "a rational immune system", "maintenance of muscle tone" and "no cancer" if you don't actually know these things work; once you get to know them better, the beauty of the solutions becomes evident. -- TomAnderson

And in "requirements" you might include the capacity for intelligent thought and spiritual introspection, if you were the sort who considered the mind-body division an arbitrary fiction.

You're asking for AI. We're obviously not there yet. Note that spiritual introspection was an accident of evolution. Our species didn't achieve it until a few millennia ago. It was not part of our design spec.

Spiritual introspection was an accident? So which of the features were on purpose? I'm pretty curious as to how you learned the design intent of whomever/whatever created HumanBeings, whether that was God or chaos or evolution or Gaia. And, hey, can you give me his phone number?

Regardless of what was intended, spiritual introspection and intelligence are part of the design we've got now. I don't know how we can call any refactoring a "refactoring" if it's not going to maintain the same functionality. -- fh

Spiritual introspection (secularly: consciousness) was not selected for by biochemical evolution. Humans were already fully evolved long before it happened. In fact, there are still humans alive today that do not have consciousness (non-functioning schizophrenics) and states of mind where consciousness is radically altered or entirely suppressed (e.g., hypnosis). Consciousness arose out of social evolution, not biochemical evolution. The fact that it was even possible is pure accident.

: I would be interested in seeing any sort of proof that Homo Sapiens Sapiens did not have consciousness when it first evolved c. 50000 years ago. Or any sort of authoritative opinion stating that schizophrenics and people under hypnosis are not, in fact, conscious. Altered consciousness != lack of consciousness.

Anyways, evolution has had billions of years and the resources of the entire planet. Is another century really too much to ask for a few humans in a handful of research labs to create AI?

: No, it certainly isn't. I was responding more to some on this page who were implying that the refactoring could be started very soon, as in today. Also trying to make the point that if the concept of RefactoringTheHumanBody should give you pause if you don't actually believe that mind and body are separate. -- fh

I think that anyone who conveyed such an attitude meant it with tongue firmly in cheek.

As for consciousness, schizophrenics describe themselves as unconscious during psychotic episodes. They start out (are raised to be) conscious then they experience the incredible panic of losing consciousness. Then we dope them up and they recover to tell about it.

The irrefutable proof that homo sapiens didn't acquire consciousness until very recently is that it is impossible to conceive of our species taking so many millennia to get to the point it is today if one posits that humans always thought roughly as we do today. How could they have spent 40 millennia achieving nothing? In fact, it is likely that homo sapiens didn't even have language a mere 12,000 years ago, never mind consciousness 50,000 years ago.

Besides, humans starting out conscious is completely impossible. Language is not a genetic trait, it had to be acquired in very small incremental steps by our stupid ancestors. And most likely in an ineffective ass-backwards way. Consciousness, being a function of language, also had to be acquired in very small incremental steps by our stupid ancestors. Even today, there are people without consciousness and even people without language (e.g., the few cases of wild children who weren't recovered before the critical age of 6 years).

You'll probably enjoy reading The OriginOfConsciousness in the Breakdown of the Bicameral Mind by JulianJaynes.

People with consciousness?! What the hell are you speaking about? The only conscious thing in the Universe is me!