Wanted: a simple explanation of abiogenesis

On the right, science. On the left, incredulity.

On Sun, Nov 6, 2016, I awoke to find this email in my American Atheists mailbox, from a gentleman writing from India:

Dear Sir, 

Good day to you.
                     
I would like to reintroduce myself as an independent researcher in philosophy and modern science. I gratefully acknowledge your previous evidence-based reply that helped me a lot to improve my critical thinking skills. 

Being an open-minded, unbiased researcher, it is my pleasure to share one of my concerns- as expressed below, hoping a satisfactory explanation: 

When we talk about consciousness, we all know that consciousness is the result of certain evolutionary arrangement of atoms. How can a specific 'collection of atoms' in the universe alone  'think', 'aware' and 'reason' about even 'its' own existence while all the sub-atomic particles in the universe are governed by the same laws of physics? 

I mean, what is the logical and rational plausibility of our assumption that physical objects (obviously they are made up of atoms and atoms don't have any self-awareness and consciousness) , for example, a rock ( or any inorganic, non-living matter of choice ) of certain mass (Kg), when subjected to blind, unconscious, unplanned and unintelligent evolutionary forces of magnitude of certain Newtons (N) for trillion, trillion, trillions of years or even infinite time , the original rock will become 'self-aware' in such a way that now the rock is able to 'think', 'aware', and 'reason' about even 'its' own existence and 'its' surroundings, able to grasp the laws of physics, mathematics, able to involve in logical reasoning, able to draw logical conclusions, able to feel sense of justice, sense of purpose and sense of existence, able to involve in rational thinking, able to feel pain and sorrow etc.?

Is there any logical fallacy in looking beyond the theory of abiogenesis?

Appreciate your kind feedback.
Please ignore and forgive me if this e-mail is an offence.

Thanks and regards,
F---- V----- P----------,
Electrical Engineer,
INDIA. 

When I read his question -- 

I mean, what is the logical and rational plausibility of our assumption that physical objects... when subjected to blind evolutionary forces... will become 'self-aware'?

-- I was tempted to write in reply, simply, "1.0", reflecting the 100% plausibility of the emergence of consciousness from non-living precursors, in light of the evidence of the physical world around us and the conscious being (myself) typing in response. I decided in the end to give him a less trivial reply. 

For your reading pleasure, here is my Sunday morning armchair musing on abiogenesis, and the emergence of thinky out of rocky, and all that jazz. 

Dear F----: 

Excellent to hear from you. I'll copy you from my personal email account, so our conversation doesn't clutter up my official inbox.  

Let me address out two points I see in your message that create a lot of confusion. 

The first objection I have has to do with your analogy likening the emergence of consciousness to a rock manifesting the ability to think. This is an error of analogy, akin to an error in understanding what is meant BY abiogenesis, and indeed, by consciousness.  

No theory of abiogenesis posits that a solid solitary object (such as: a rock!) would within its own geological lifetime undergo such physical changes that allow it eventually to think, while also retaining its identity AS a rock. 

Abiogeneis as it is currently conceived is not a local phenomenon that occurs WITHIN an ecology -- today you have no life, and tomorrow, there it is, there is life, isolated and localized within, and somehow separate from, the ecology. Rather, abiogeneis is a process that occurs over geological timescales, and in a manner distributed throughout systems that span an entire ecology. Further, it is conceived of as an incremental process, with manifold different simultaneous instantiations.  

The popular image of abiogenesis as having to do with a puddle of slime on a rocky shore, as isolated in its reaction space as a glass beaker in a lab, is wildly misleading. Although there needs to be a certain degree of concentration of reagents and stock materials, and a certain patterning to the encounters different chemical (and eventually, biological!) materials undergo, this does not bear comparison to the slime puddle image. Things are altogether more dynamic, and take place at scales that are at the same time much smaller (microscopic clay templating! RNA self-catalysis!) and much larger (ocean depth gradients of iron- and sulfur-bearing isoclines! or, according to a different model, iuron- and sulfur-bearing surface deposits such as those surrounding ocean floor vents).  

In other words, I fear that your metaphor of abiogenesis operates at the wrong levels of scale, and with the wrong impression of dynamism. 

The other point I'd wish to address briefly, in response to your kind invitation, has to do with your presentation of the concept of "consciousness." This, like abiogenesis, is a complicated subject which is sometimes disfavored by limiting metaphors. 

You write:  

now the rock is able to 'think', 'aware', and 'reason' about even 'its' own existence and 'its' surroundings, able to grasp the laws of physics, mathematics, able to involve in logical reasoning, able to draw logical conclusions, able to feel sense of justice, sense of purpose and sense of existence, able to involve in rational thinking, able to feel pain and sorrow etc.?

This, on its surface, sounds like a plainly ludicrous proposition. But I'd never describe consciousness in this manner. Instead, I might translate your description this way:
the original rock may be subjected to the processes of weathering and erosion, such that it is reduced to sediment. The minerals and chemicals which constituted that rock are now available to circulate in the (aqueous, likely) ecosystem, where they may be involved in chemical reactions we believe to be preliminary to the abiotic formation of biological monomers, such as carbon fixation, chemical reduction, or (to give a more complex example), pyramidine formation.  

Over time, an ecology which has produced biological monomers, may enter into a state of conditions conducive to the formation of biological polymers, some of which are self-catalyzing. The abiogenesis really heats up then!
An ecology which features concentrations of self-catalyzing biological polymers may give rise to autocatalytic chemical networks and structures such as micelles and vesicles. These molecular-scale phenomena may interact and form more complex structures and systems, which we begin to recognize as rudimentary "proto-life."  

Over eons of chemical, and then biological, and then ecological, evolution, this proto-life may develop adaptive systems which "record" life experience, in the form of chemical changes in the cell, or taxic changes in behavior, or changes in genetic expression, or charge potential changes in nerve cells. As this system of record-keeping (memory, you could call it) becomes more sophisticated, the organism benefits from the ability to predict appropriate behavior for future conditions which resemble past conditions it has a record of. This is a significant part of what we call learning.   

The organism continues to become more sophisticated. But keep in mind, we aren't talking here about a single individual. We are speaking in evolutionary terms, so this change takes place over countless generations, across the somatic instances of countless individuals.  

Eventually, the learning/memory systems of the organism become so sophisticated, and recursive, and powerful, that the organism is able to model future potential behavior! This does bear comparison to the way that a computer program using patterns of charge distribution in an electronic system, to model the world of a computer game. We don't think there's anything magical about that, do we? Likewise, the pattern of charge distribution in the nervous system of the organism, are able to run a model of the world. And this model may contain sub-programs we can label as "thinking", "awareness", "reasoning about its own existence and its surroundings", "pondering the the laws of physics", "mulling over maths", "fiddling about with logical reasoning", "the drawing of conclusions", "the sense of justice", "a sense of purpose" , "a sense of existence", and "the experience of pain and sorrow."  

All of these thoughts and feelings are 1) simply patterns of charge distribution changing across the vastly complex representational network of a nervous system, and 2) amazing. 

Voila! From rock to mind. Now, I am kidding, of course. But I hope that my "translation" of your description of the origin of consciousness, even as briefly as I describe it, is enough to make the point I intend -- namely, that while there is so much that we have yet to measure, verify, and truly understand about the way life emerges from non-life, and how mind emerges from minerals, the nature of the mystery isn't, any longer, metaphysical, if we come to terms with the vast scales of complexity involved in a naturalistic explanation.  

Seen from a distance, the complexity of the naturalistic explanation may look supernatural. But we don't have to keep our distance. We can zoom in, get our hands and minds dirty, and engage with data, and models, and articles and animations and questions and answers, and so on, through the technology of information and communication which frees us from the backwaters of our ignorance as separate individuals. (That internet -- she's amazing.) 

Thank you for the stimulating questions; these were fun things to think about on a Sunday morning here in New England. 

With warm regards from Boston, 

Zachary "the Thinking Rock" Bos
Massachusetts State Director for American Atheists

To the extent that we atheists want to have our materialist apologetics in order, I think it would be useful to have a "best practices" way of responding to questions like, ah, but, rocks can't think, can they.

Do you have any suggestions for concise and accessible explanations of abiogenesis, of the sort we could share with persons like this Indian engineer when they have questions about the plausibility of that theory? I'd love to know what you recommend. (How great if there was a really brilliant YouTube animation going through this stuff... )

The graphic above, interestingly enough, comes from the blog of a Christian defending creationism as a plausible theory.

(Authored by Zachary Bos. Cross-posted from the Atheology blog.)

Blogger skeptical & compassionate, if unfair toward antitheists. Also, dragons.

Blogger Lindy West, responding to a creationist's argument that dragons were literally real:

Now, I don't personally believe in Satan (or dragons, or demons, or resurrection, or underground pits of eternally burning gay people, or that a guy can build a campfire in a whale's colon), but I don't mind if people do as long as their commitment to literalism remains wholly separate from my country's legislation and scientific progress. I recognize that religious beliefs, institutions, and structured rituals—even ones that seem arbitrary to an outsider—can be extremely fortifying for people, especially communities of people that have been abandoned or demonized by the status quo.

On the one hand, this is a great succinct example of sound and healthy skepticism. On the other hand, West is implicitly throwing critics of religion under the bus (specifically, those critics who do mind if people believe in supernatural entities, and who think that such belief helps to normalize certain undesirable and dangerous attitudes and behaviors).

On the other other hand, she acknowledges the benevolent role religious participation can play in believers' lives, without endorsing said supernaturalism. Two out of three ain't bad! (via Jezebel)

*

And, how could we deprive you of the opportunity to watch a guy argue for the existence of dragons on theological grounds? Here's the video from the Jezebel post:

Creationist lecture this Sunday

When was the last time you stopped to think about why you believe in evolution? Join Nathaniel Jeanson, Harvard PhD in Biology, THIS SUNDAY in Boston, an in-depth look at his reasons for thinking that modern biology has failed to substantiate Darwin's evolutionary hypothesis. Q&A to follow.

Free admission and free parking available at the center -- look for signs.

Jeanson has given this presentation before -- get a full report from a BA member, at http://bostonatheists.blogspot.com/2009/08/report-on-nathaniel-jeansons.html.

You can download full audio files for the lecture and Q&A session at http://w74.org/ij.

The Boston Atheist Examiner wrote it up (http://www.examiner.com/atheism-in-boston/reports-from-a-creationist-lecture-boston) and a letter I circulated about the lecture was posted at Richard Dawkins' website (http://richarddawkins.net/articles/4176).

The Institute for Creation Research thought we Boston Atheists weren't very open-minded last time: http://www.icr.org/article/harvard-phd-lecture-exposes-prejudices. This time around, we can be even more open! Open, that is, to establishing ties with members of the congregation, and being open to finding ways to help them avoid being misled by Creationist flimflam.

Where: Longwood Galleria Conference Center, 42 Longwood Avenue Boston, MA (accessible via the mall food court)
When: Sunday, March 27, 2011, 6:30 PM

Sponsored by http://calvarychapelinthecity.com/.

RSVP at http://www.meetup.com/bostonatheists/events/17048404/

A Report on Nathaniel Jeanson's Creationism lecture

Member Steve Wertheim went to the 7:00 session of yesterday's lecture at the Calvary Chapel in the City worship service, a program entitled "Evolution: Bankrupt Science. Creationism: Science you can bank on" on 8/16. He wrote a report on his observations for the BA message board, which corresponds in large degree to my own experiences at the earlier presentation of the same lecture earlier that day. He writes:

In front of a church group audience, seemingly composed of young people with no background in science, Dr. Nathaniel Jeanson, a recent PhD graduate of Harvard:

1. Distorted the nature of science and the scientific method.

2. Distorted the meaning of actual scientific work, such as that of the Harvard paleontologist Stephen Jay Gould.

3. Denied the reality of the single most important unifying concept in biology, that of evolution by natural selection.

4. Presented junk science as reliable, such as that of Michael Behe, John Morris and Russell Humphreys.

5. Repeated discredited arguments for the existence of the supernatural, such as "irreducible complexity". For this he used his own research, claiming that the 6 interacting components in the vitamin D regulatory cycle could not have been produced by evolution and must have been created by a supernatural intelligence.

6. Appealed to what has been termed the "argument from ignorance" (reflecting his intellectual limitations). His comment on Vitamin D regulation was "It is difficult to conceive how you could evolve this". I don't claim to be an expert in this field, but I do know that evolutionary mechanisms for all examples of "irreducible complexity" claimed by Michael Behe (a crackpot with tenure who originated the idea) have been provided by real scientists.

[This is especially baffling, consider how well a job I thought I did in the morning presentation at walking him through a rebuttal of all arguments that work from the grounds of "irreducible complexity" (IC). If all science is based on observation, and only on observation, as Jeanson said at the start of his lecture, then it is irrational for a research to look at a complex system and label it IC. To make this claim is to assert that we have been able to observe all the precursor systems that led up to the current system, and that in all of that evolutionary history, there were never any components that are now missing but which when present would have allowed for reducible complexity. The analogy I made was to a stone arch; remove a stone and the structure collapses, but we could only call it irreducibly complex if we failed to realize that there was once a scaffold that allowed the thing to be built in a step-wise fashion, stone by stone. IC is at best an admission of ignorance, but in no circumstances can it be construed as a meaningful biological term. It literally describes nothing. Jeanson might have understood this before his lecture or he might not, but after our exchange he has no excuse for using the same reasoning at the later lecture. -- Zachary Bos]

7. Claimed that "eyewitness accounts" are the most reliable, in science as in a court of law. In fact, eyewitness accounts in legal proceedings are notoriously unreliable, and there would not be much science if we only had our eyes to rely on. But the kicker is that the real points he was making were:
a. The eyewitness account of Yaweh, who was present at the creation, is the most reliable information we have about origins.

b. "One cannot answer historical questions scientifically", because there were no eyewitnesses.

8. Stated that his "colleagues at Harvard" view the lack of a demonstrable mechanism for the origin of life from non-life as the "worst evolutionary problem".
[Is this view shared by former supervisor, Dr. David Scadden of the Harvard Stem Cell Institutce, or by Dr. Catherine Dulac, Chair of the Dept. of Molecular and Cellular Biology at Harvard? -- Z.B.]

9. Made a series of outrageously false claims outside his research field, including:
a. The Earth is 6,000 years old, because the Bible tells us so.

b. There are "no direct scientific measurements for the age of the Earth".

c. The Earth is "at or near the center of the universe".

d. Radiometric dating of rocks (and therefore the accepted age of the Earth) is fatally flawed and can lead to a measured Earth age of 6,000 years as easily as an age of 4.6 billion years.

e. "Evolution says the Big Bang occurred 15 billion years ago." (Two mistakes in one sentence!)

f. Radioactive decay probably happened at an accelerated rate in the past.

g. Geologic formations such as the Grand Canyon and bio-geologic formations such as coal, can and do form rapidly and "catastrophically".

h. There are few, if any, transitional forms in the fossil record.

i. The mind is not a direct product of brain activity, and in fact, to suggest that the mind is directly related to the brain is a "self-defeating statement".

j. Living species did not evolve from a common ancestor, based on molecular biologic evidence. He used comparisons of the cytochrome c protein sequence for this, and ignored the whole genome sequences available for many of the same plants and animals. This was an especially unconvincing tactic for someone who claims to be a biologist.

Suffice it to say that each and every one of his points was either a distortion (e.g. Stephen Jay Gould's theory of "punctuated equilibrium" exposes a weakness in evolutionary theory), an irrelevant red herring (e.g. evolution leads to immorality), or an outright lie (e.g. there are few, if any, transitional forms in the fossil record).

His ignorance of anything outside the creationist literature, coupled with his intellectual arrogance was truly shocking for someone who claims to be educated.

All of this would be laughable if it were not in front of a credulous audience, if the percentage of people who believe in creationism in the US were not at a steady 45% and if the responsible teaching of science in our public schools were not under continual attack from people such as Dr. Jeanson.

His performance in the Q&A session was no better.

1. When asked if his religious views affected how he practices science, he said that while he does not believe that the vitamin D regulatory loop evolved, the question never came up in the course of daily research. Of course I know that the big questions are not the stuff of most daily research, but when I was a graduate student, all we talked about at the bench, while doing our monotonous tasks, were the big questions – the principles, the hottest new research and what the latest Science or Nature paper meant. It's a shame that Nathaniel Jeanson was impervious to this crucial part of his education. It's a shame he missed out on appreciating the central organizing principle of biology, and one of the greatest achievements of the human mind.

2. He was asked if he was aware that 2 sets of Nobel Prizes have been given for the confirmation of the Big Bang; that the theoretical underpinnings were provided by Einstein, Gamow, Friedmann, Weinberg and Hawking; that a 13.7 billion year age for the universe is accepted by all working physicists; and that (contrary to his claim that one cannot answer historical questions scientifically) the COBE and WMAP satellites have provided pictures of the early universe 400,000 years after the Big Bang. He merely responded that his “colleagues" at the ICR (meaning Russell Humphreys) have "alternative explanations" for these data. When asked if this means that Russell Humphreys is smarter than Einstein and Hawking, he had no answer.

3. When asked about the fossil hominids, he repeated the creationist canard that they are either apes or humans, not transitional forms.

4. When asked about the genome sequencing and bio-informatics work of Prof. Eric Lander of the Broad Institute and MIT, which demonstrates common ancestry and species relationships through analysis of genome sequencing data, he had no response and moved on to another question.

Apparently this is all part of his career path, as he is giving out business cards from his new position at the Institute for Creation Research - a set of hilarious crackpots who claim they are doing "research" that supports the inerrancy of the literal Bible. Of course, they know the answer already, now they are just trying to make the data fit the result they want. Since this is difficult, what they primarily do is write treatises about how science is a conspiracy, why the NSF and NIH grant committees won't fund them, and why no actual journals will publish their "research".

At the ICR, I'm sure that Dr. Jeanson will be well paid, while doing no publishable research, merely because he has a Harvard degree and there is an audience for his message. He will be "banking on" it. I wouldn't be surprised if some of his grad school income came from the ICR all along. It should cause all of us to be wary of the tactics of these intellectually and morally dishonest people.

Thanks for the reporting, Steven. Another first-hand report is up on the Pharyngula blog. Readers may want to grit their teeth and visit CreationWiki, "a free encyclopedia of apologetics that is being produced by an international team of missionaries." Sounds very scientific.