How Can We Use Engineering to Elucidate Biology?

_{Jonathan Bartlett

September 13, 2012

Intelligent Design}

Share: Facebook; Twitter; LinkedIn; Flipboard; Print; Email

Engineering is, by definition, a teleological effort. Things are done in order that something else may happen. I have wondered how biology might be improved by taking ideas, practices, and methodologies from engineering and applying them to biology.

Any ideas?

NOTE – I accidentally used the word “approved” rather than “improved” in the post. This is fixed. Sorry for the confusion.

Comments

As well johnnyb, this should be of interest to you:
Researchers find retinal rods able to detect photon number distribution - September 14, 2012 Excerpt:,,, In the study, the team fired a rapid succession of laser pulses at the rod and found it able to discern, i.e. measure, individual differences of up to 1000 photons per pulse. They also found that the rods were able to tell the difference between coherent light (the degree to which the waves are in phase) and "pseudothermal" light, where the waves are chopped up by a rotating disk, to such an extent that the researchers believe they will be able to serve as a model for creating highly sensitive artificial detectors. In the end, the researchers found that single rhodopsin molecules are able to interact with single photons, a finding that demonstrates just how sensitive rods truly are; so much so that further studies by the team will look at their use in quantum optics and communication. http://phys.org/news/2012-09-retinal-rods-photon.html
bornagain77_{September 14, 2012
September
09
Sep
14
14
2012
01:26 PM
1
01
26
PM
PDT}

johnnyb, 'serendipitously' this just came up on physorg:
From vitro to vivo: Fully automated design of synthetic RNA circuits in living cells September 14, 2012 Excerpt: Synthetic biology combines science and engineering in the pursuit of two general goals: to design and construct new biological parts, devices, and systems not found in nature; and redesign existing, natural biological systems for useful purposes. For synthetic biologists a key goal is to use RNA to automatically engineer synthetic sequences that encode functional RNA sequences in living cells. While earlier RNA design attempts have mostly been developed in vitro or needed fragments of natural sequences to be viable, scientists at Institut de biologie systémique et synthétique in France have recently developed a fully automated design methodology and experimental validation of synthetic RNA interaction circuits working in a cellular environment. Their results demonstrate that engineering interacting RNAs with allosteric behavior in living cells can be accomplished using a first-principles computation. http://phys.org/news/2012-09-vitro-vivo-fully-automated-synthetic.html
bornagain77_{September 14, 2012
September
09
Sep
14
14
2012
01:18 PM
1
01
18
PM
PDT}

InVivoVeritas: Ah yes, thanks for the reminder. I remember some of those discussions, as well as the work you did, which was of particular interest to me because I'd spend a fair amount of time (mostly mental, not so much in written form) thinking about what would be required for the simplest SSR. I think you have some great thoughts. A similar exercise would be a valuable undertaking for anyone who has a deep interest in the origin of life. I also remember looking at Szostak's site and some of his materials in a fair amount of detail, primarily at the insistence of Elizabeth Liddle who was very enamored with Szostak's work and thought it was much more supportive of a materialistic origins theory than it actually was. Szostak is doing some good science, but at the end of the day his work will be yet another demonstration of just how distant from reality the materialistic origins myth is. BTW, if anyone is onlooking and hasn't looked into this issue before in detail, I would definitely recommend taking a bit of time to check out the links InVivoVeritas cites.Eric Anderson_{September 14, 2012
September
09
Sep
14
14
2012
01:08 PM
1
01
08
PM
PDT}

Mung @10: Excellent questions, stated simply and straight-forwardly from an engineering point. I also like your focus on energy and work. In addition to being fundamental issues, stating the problem that way gives the lie to the silly "but Earth is an open system" argument often heard from materialists. (Note, I'm neither endorsing nor criticizing Sewell's work or any other thermodynamic-challenge-to-evolution ideas, just highlighting the absurdity of thinking that more raw energy is the answer to the problem.)Eric Anderson_{September 14, 2012
September
09
Sep
14
14
2012
12:54 PM
12
12
54
PM
PDT}

Eric In essence this is the approach I took, when I encountered on UD blog the discussion of the interview with Jack Szostak: https://uncommondescent.com/intelligent-design/software-engineers-off-the-cuff-requirments-list-for-simple-cell/ In that interview he kind of claimed that since he (thought that he) elucidated the materialistic origination of the cell membrane, he is HALF-WAY for resolving the Origin of Life problem. The discussion on the UD blog prompted me (as a software engineer) to start an investigation of my own on how I should design a Simplest Self Replicator (SSR). The result of that investigation is this presentation at the Engineering and Metaphysics conference in June 2012: https://uncommondescent.com/intelligent-design/the-design-of-the-simplest-self-replicator/ The investigation was very interesting and instructive. Here are a few lessons I learned: • The design of the SSR is very (extremely) complex • Implementation of a fully autonomous artificial SSR is clearly (much) beyond our current level of engineering and technology • We should have legitimate engineering /scientific reasons to praise the Designer of Life Now coming back to johnnyb's topic: • Any engineering effort to elucidate biology starts from the conviction that we will discover mechanisms, machinery, information and information processing that make sense and are structured to achieve specific goals and purposes. • This conviction is founded on observing external behaviors of living organisms - that are effective and accomplish goals. • It seems that cell biology still needs to (fully) elucidate many cell mechanisms. Two examples: 1. How information is communicated between cell entities in support of cell processes? 2. Where is stored the information for the “body plan” of an organism?. Note that even a single-cell organism should have a body plan that will specify where to “place” various cell parts being constructed during cell replication and how to “link” or organize these parts between them. • For 1. above: As a a software engineer I know that any complex system with multiple functioning parts MUST have proper way to communicate information. And this may imply solving information representation, coding, serialization and de-serialization, transport protocols, etc. And I believe it is absolutely rational to expect that the cell possesses equivalent information communication means. • For 2. above: As a (software) engineer I know that the construction of any complex artifact, made from multiple types of components, organized following a particular manner MUST follow a blue-print or a construction plan – that, in essence, is STRUCTURED INFORMATION (or CSI). So I have rational motives to expect that such information MUST exists – in a form or another – somewhere in the cell (IMPORTANT NOTE HERE: this is kind of STRONG materialistic thinking. Would it be possible that this information resides SOMEWHERE OUTSIDE THE Cell, but still EXISTS? This hypothesis is not so materialistic).InVivoVeritas_{September 14, 2012
September
09
Sep
14
14
2012
11:25 AM
11
11
25
AM
PDT}

Eric - Ah! I mistype. It was supposed to be "improved". Yes, you are exactly correct. I think there is one ID professor which asks their student to design an airway which is more efficient than our present one, but still avoids the problem of choking. It's actually pretty phenomenal.johnnyb_{September 14, 2012
September
09
Sep
14
14
2012
10:47 AM
10
10
47
AM
PDT}

I need energy in order to function. Where does that energy come from? How does it get imported into the system? How is it converted into work? These are all absolutely fundamental to not only engineering problems but life itself. Like Eric says, It would be instructive to see how the most basic cell solves that problem, and then ask what did it take to bring about that very fundamental system in the first place.Mung_{September 14, 2012
September
09
Sep
14
14
2012
10:00 AM
10
10
00
AM
PDT}

johnnyb: I'm not sure what your question means (". . . how biology might be approved . . . ?) But if you are talking about taking what we know of engineering and applying it to biology (rather than the other way around as ba77 suggests), I have long thought that if I were a professor teaching a semester-long biology course I would love to take a specific problem (the need to clot blood; sight; smell; hearing; RNA translation; whatever) and have the students spend at least a good portion of the semester coming up with a solution. I don't mean some kind of high-level hand-waving solution. I mean a real engineering-level, detailed, functional solution. Starting from scratch, looking at available materials, the biochemistry involved, switches required, feedback mechanisms, and so on. I'm convinced that it would be (i) absolutely sobering what is actually involved in getting a functional system, and (ii) awe-inspiring. As an added benefit, it might also inocculate the students against the silly "just-so" stories of the materialist creation myth. Forever after when they heard such a story they would ask "OK, but which molecule are you talking about and exactly how does it interact with the other molecules to do x?"Eric Anderson_{September 14, 2012
September
09
Sep
14
14
2012
07:50 AM
7
07
50
AM
PDT}

JohnnyB: See why I focus on the informational content involved in designs and its implications? FSCO/I is functionally specific, complex beyond a threshold where blind chance and necessity are reasonable as explanations, and directly or indirectly -- nodes and arcs frameworks converted into descriptive strings -- informational. We routinely observe its cause in the world of technology, and we see from the vNSR what would be required to put it into a self-replicating machine. We see direct parallels int eh world of the cell. It is then very reasonable to infer that the best explanation of what we see but where we did not observe at its origins, is the same as what we see all around us in the process of being built: intelligently directed organising work. Especially, given that blind chance and mechanical necessity will have enormous search space challenges on the gamut of the solar system or the observable cosmos. KFkairosfocus_{September 14, 2012
September
09
Sep
14
14
2012
06:31 AM
6
06
31
AM
PDT}

Well johnnyb I certainly agree with that very sensible approach to integrating Engineering and biology. It certainly will be much more fruitful than the current Darwinian paradigm which, instead of appreciating the marvels we find in life, and trying to find a fruitful approach that may benefit man from the integration of the two, the Darwinian paradigm many times tries to falsely claim that, for purely theological reasons (C. Hunter, P. Nelson), that life is nothing but kludged together junk. Moreover, as I'm sure you well know, this is done just so to try to establish itself as scientifically legitimate. Notes:
William Bialek - Professor Of Physics - Princeton University: Excerpt: "A central theme in my research is an appreciation for how well things “work” in biological systems. It is, after all, some notion of functional behavior that distinguishes life from inanimate matter, and it is a challenge to quantify this functionality in a language that parallels our characterization of other physical systems. Strikingly, when we do this (and there are not so many cases where it has been done!), the performance of biological systems often approaches some limits set by basic physical principles. While it is popular to view biological mechanisms as an historical record of evolutionary and developmental compromises, these observations on functional performance point toward a very different view of life as having selected a set of near optimal mechanisms for its most crucial tasks.,,,The idea of performance near the physical limits crosses many levels of biological organization, from single molecules to cells to perception and learning in the brain,,,," http://www.princeton.edu/~wbialek/wbialek.html "Organisms are not cobbled together as a series of adequate compromises but are close to optimality. Examples of supposedly “poor design” often turn out to be “very well engineered indeed”. Simon Conway Morris http://darwins-god.blogspot.com/2012/04/even-evolutionists-admit-its-mess.html Peacefulness, in a Grown Man, That is Not a Good Sign - Cornelius Hunter - August 2011 Excerpt: Evolution cannot even explain how a single protein first evolved, let alone the massive biological world that ensued. From biosonar to redwood trees, evolution is left with only just-so stories motivated by the dogma that evolution must be true. That dogma comes from metaphysics, http://darwins-god.blogspot.com/2011/08/peacefulness-in-grown-man-that-is-not.html The role of theology in current evolutionary reasoning - Paul Nelson http://www.springerlink.com/content/n3n5415037038134/ Charles Darwin, Theologian: Major New Article on Darwin's Use of Theology in the Origin of Species - May 2011 http://www.evolutionnews.org/2011/05/charles_darwin_theologian_majo046391.html
bornagain77_{September 14, 2012
September
09
Sep
14
14
2012
06:27 AM
6
06
27
AM
PDT}

BA77 - I don't disagree, but think about it this way - we know very little of the design of biology. We are much more intimate with our own works. We know the history of what we have done, and what problems must be avoided to avoid disaster. Looking at the design of biology de novo, we wouldn't necessarily know what each piece does, because we weren't the ones that built it. However, as we have grown in the engineering disciplines, we have established many general principles. Therefore, as we investigate biology, I think it is useful to compare it to the known general principles to help elucidate what we don't know.johnnyb_{September 14, 2012
September
09
Sep
14
14
2012
05:39 AM
5
05
39
AM
PDT}

Niwrad My first instinct is to agree with you. But if I sit and reflect seriously, I'd try to avoid the dichotomy altogether and use the strengths of both approaches. I'm deeply suspicious of the possible bridge from "super-engineering" to a "super-engineer": one has to remember that engineers don't use the phrase "Let there be..." to produce things. Yet the recognition of design, as Steve Fuller says, goes beyond mere analogy to an identity of what happens in nature with what we do as rational beings. But not completely beyond analogy, in my view. Similarly nearly everyone accepts some role for natural selection, at least at the micro level, which engineered objects are not really able to emulate except in those weird design algorithms. And if Shapiro's anywhere near right, ignoring that side might result in our being left behind in understanding how the Designer is interacting with his materials in ways that go beyond engineering, just as creation ex nihilo goes beyond it.Jon Garvey_{September 14, 2012
September
09
Sep
14
14
2012
04:53 AM
4
04
53
AM
PDT}

How Can We Use Engineering to Elucidate Biology? You should ask that question to Dr. Adrian Bejan, professor of mechanical engineering and thermodynamics at Duke University. Sure, he rejects Intelligent Design theory as a 'fantasy'. But he believes/accepts in 'design in nature' and insists 'design' is a 'scientific' concept. So, it would see you should want to ally with his pro-science position. I wrote about his view of 'design in nature' vs. ID's view of 'design in nature' here: Whose Notion of 'Design in Nature' do you accept? "Engineering is, by definition, a teleological effort." - johnnyb Yes, it is also by definition a social effort. As a scientific field, biology is also a teleological effort; to understand, explain and even to control the biosphere for the purpose of improving human knowledge and living. Are there *any* sciences that are by definition 'non-teleological'? Please let me know of what you consider (a) 'non-teleological' field(s), according to your definition of 'teleology' and 'science,' johnnyb.Gregory_{September 14, 2012
September
09
Sep
14
14
2012
04:36 AM
4
04
36
AM
PDT}

Jon Garvey, If carefully examined, all your "limitations of the parallel" indeed strengthen the view of biology as super-engineering, rather than evolutionist non-engineering.niwrad_{September 14, 2012
September
09
Sep
14
14
2012
03:51 AM
3
03
51
AM
PDT}

I'm not an engineer (maybe that's a good thing) but a few thoughts. Organisms and their organs/organelles have to do work in the same physical world as machines, so they are bound to use similar priciples. That's never been in doubt - bones were known to be levers long before flagellae were seen as motors. Also, there is a parallel in that design can be seen as "intellectual property" rather than simply as physical features. However, the limitations of the parallel need to be recognised, as some ID critics have pointd out. A few are: (a) Biological machines work in a liquid/gel state and, moreover, seems to be called into actual existence when needed. That doesn't happen with cars. (b) There are different constraints on things that grow into existence, and reproduce, from those that are assembled from parts each time. (c ) The latest biology hints at internal teleology: a cell needs to do "A" and may get there in different ways if the first choice is blocked. Machines are not teleological in that sense. (d) An evolutionary process, even a guided one, imposes somewhat different constraints from a factory-based R&D process. (e) A direct act of creation would also have implications for design/assembly processes. (f) An omniscient designer does not work by trial, error and progressive development(though he could conceivably initiate a process that did so). One needs therefore to assess "errors", "bad design" etc in a different manner from human engineering.Jon Garvey_{September 14, 2012
September
09
Sep
14
14
2012
02:17 AM
2
02
17
AM
PDT}

Not to seem flippant johnnyb, but since the systems and machines that are being found in biology exceed what our best engineers have produced thus far shouldn't the question really be,, "How Can We Use Biology to Elucidate Engineering?" notes:
"Biomimetics and the Positive Implications for Intelligent Design" - Podcast - September 2011 http://intelligentdesign.podomatic.com/entry/2011-09-23T15_43_04-07_00 Eyeballing Design "Biomimetics" Exposes Attacks on ID as Poorly Designed By: Casey Luskin - December 2011 Perhaps the most familiar example of biomimetics is the body shape of birds serving as the inspiration for aircraft design. But the list of fascinating cases where engineers have mimicked nature to develop or improve human technology goes on and on: • Faster Speedo swimsuits have been developed by studying the properties of sharkskin. • Spiny hooks on plant seeds and fruits led to the development of Velcro. • Better tire treads were created by understanding the shape of toe pads on tree frogs. • Polar bear furs have inspired textiles and thermal collectors. • Studying hippo sweat promises to lead to better sunscreen. • Volvo has studied how locusts swarm without crashing into one another to develop an anti-collision system. • Mimicking mechanisms of photosynthesis and chemical energy conversion might lead to the creation of cheaper solar cells. • Copying the structure of sticky gecko feet could lead to the development of tape with cleaner and dryer super-adhesion. • Color-changing cuttlefish have inspired television screens that use a fraction of the power of standard TVs. • DNA might become a framework for building faster microchips. • The ability of the human ear to pick up many frequencies of sound is being replicated to build better antennas. • The Namibian fog-basking beetle has inspired methods of desalinizing ocean water, growing crops, and producing electricity, all in one! http://www.discovery.org/a/18011 Biomimetics and the Design of the Eye - podcast http://intelligentdesign.podomatic.com/entry/2011-12-21T14_03_45-08_00
bornagain77_{September 14, 2012
September
09
Sep
14
14
2012
01:27 AM
1
01
27
AM
PDT}

Prev 1 2

You must be logged in to post a comment.

Leave a Reply