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Rob Sheldon on the genome map mess

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Rob Sheldon

Recall the genome mapping mess that Kas Thomas alerted us all to? Physicist Rob Sheldon writes to say that we should pay attention to what Thomas is saying here:

What it tells us, is that modern “annotation” tools for finding genes in the database of transcribed codons, use iterative methods that have to be “trained”. Sort of like the way speech recognition programs have to be trained. Nothing wrong with that, there are all sorts of reasons why iterative processes are efficient and effective. However, they are not deterministic. There is not a fixed “rule” that determines the output. Instead, the “rules” are fuzzy logic based on a set of examples, a “training set”.

Okay, now we get to the nub of the problem. If errors creep into the database, then they get used the training set, and then even more errors are made, until the percentage of errors grows to some limiting value. However, if the database itself is being expanded at an exponential rate, then early errors propagate exponentially, so that there is no limit to the percent corruption of the database. From the charts in this blog, the annotations in the genome data base are now over 50% wrong, they are more often wrong than right.

And this is exactly what is happening to all science fields. Materialism is a bad philosophy that allows “what is observed” to replace “what exists”, because it has no correction algorithm, for example, nothing to tell evolutionary biology that “what is observed” must be fragmentary and unusual and not a rule of nature making competition between close cousins inevitable.

Instead, science makes a model, baptizes it with “reality” and then bases models on the models, all the while “tuning” the models to match the observations. These enormously complicated curve-fits in multi-dimensions are then equated with reality because they can be made to fit the observations, just like 11 epicycles were used before Copernicus to explain the motion of Jupiter.

How did we get in this mess? By making careers dependent on “research”, by tying the funding to the acceptance of “standard models”, by refusing to allow teleology into our observations, by claiming that a 5 parameter fit to the data was a “better model” than a 1-parameter fit which was “fine tuned”. And like the genome database, the models become the “training set” for the next set of models, until we have an elaborate epicyclic universe with boundless error.

How do we escape this mess? By going back to basics, to deterministic models not based on other models–eg. philosophically based foundations. By not tying funding to acceptance of peers. By not tying careers to research dollars received. By recognizing all the ways in which positive feedback encourages the exponential explosion of error, and making an institutional and foundational change to prevent it. Sort of like the unwritten rule that professors who get a PhD at an institution are barred from teaching there.

But that goes against the entire superstructure of post-WWII science that gave us all the marvels of the 21st century!

Yes it does. Some positive feedback parasites are decadal, some generational. This is a generational one. It is time for us to address it so that, like marrying your cousin, it doesn’t come back and kill us in 30 years. Science and careers are 2nd cousins. Science and government are 1st cousins. It’s time for some consanguinity laws.

The end of everything is in its beginning, they say. The science that put people on the moon has degenerated to speculation about why ET isn’t returning our calls and how many multiverses can be crammed into a black hole.

Readers, thoughts?

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4 Replies to “Rob Sheldon on the genome map mess

  1. 1
    Dr JDD says:

    The peer-review and funding systems are broke, regardless of what you think about errors or holding to theories. They are broke independent of that. These sorts of issues merely serve to further break an already broken system.

    Careers come down to luck and trend. If something is trendy, you ride that bandwagon (mostly like – in the right place at the right time), you get the funding, build up your name, get the high impact publications and your career is set. Note – none of that is related really to the skill or “best scientist” that we akin to those high “quality” publications. Often the most successful PI’s or group heads are those that are the best salesman/women. After all, you have to sell your research to a board/panel (where politics already play a role, who you know more than what you know) competing with 100s of other applications. Some funding bodies are down to 5% success rate where as not too long ago the average grant success rate was 25%. That puts enormous pressure on young researchers (and old) to conform, especially when tenure is virutally unheard of these days without a Nature or Science publication.

    When everything is reviewed (grants, publications) by current “leaders” and board members who stand by current concenses are always right then how can anyone publish/research alternative models or even get into research that challenges dogmas where they need challenged?

    As said, if something is not trendy, it is difficult. I knew a Prof when I was doing my PhD who was researching MRSA and it became big. Suddenly he had papers published in Science, he was on the news, he had funding left right and centre and he had job offers plus his own spin-off. Last I heard he was struggling to get any grants. MRSA is no longer as trendy. That’s science for you.

    I have met and worked alongside and even co-supervised PhD students who in no possible way would have gotten their PhD if they had done it 30 or 40 years ago. It is so simple to get a PhD these days in biological sciences. It is expected, a given if you want to stay in the field. Do 3 years of not-very-good research that largely is directed by post-docs and your lab head, write it up (which is then butchered to a readable version by post-docs and supervisor who doesn’t want to look bad for having a failing PhD student from their lab) and get a good internal/external for your thesis defence and congrats, you are a Dr, the future of science yet you cannot critically reason why a cell should do this rather than that.

    It is a truly depressing state of affairs. The problem is there are many brilliant scientists but if you have a stifling environment, a limited scope on what you can study, research, publish and narrow-minded views on concensus and dogma, those few brilliant scientists can sadly and all to easily, get lost in the noise (appropriate pun?).

  2. 2
    Dionisio says:

    Here’s a relatively recent publication that seems to deal -at least partially- with the discussed subject:

    Genes, structuring powers and the flow of information in living systems

    Biology & Philosophy

    May 2014, Volume 29, Issue 3, pp 379-394

    Abstract

    Minimal genetic pre-formationism is defended, in that primacy is ascribed to DNA in the structuring of molecules through molecular codes. This together with the importance of such codes for stability and variation in living systems makes DNA categorically different from other causal factors. It is argued that post-transcriptional and post-translational processing in protein synthesis does not rob DNA of this structuring role. Notions of structuring causal powers that may vary in degree, of arbitrary molecular codes that are more or less realized, of partial templating and of genetic information as a subspecies of mechanistic information are brought in to support this and to rival causal and semantic notions of information. It is concluded that the primacy of genes in their structuring of molecules goes together with parity between genes and non-genetic causal factors in regulation of living systems. This is seen to hold independently of the radical reconceptualization of organism cum environment that has been suggested in developmental systems theory.

    http://link.springer.com/artic.....013-9407-x

    Biology & Philosophy

    ISSN: 0169-3867 (Print) 1572-8404 (Online)

    Description

    Recent decades have witnessed fascinating and controversial advances in the biological sciences. This journal answers the need for meta-theoretical analysis, both about the very nature of biology, as well as about its social implications. Biology and Philosophy is aimed at a broad readership, drawn from both the sciences and the humanities. The journal subscribes to no specific school of biology, nor of philosophy, and publishes work from authors of all persuasions and all disciplines. The editorial board reflects this attitude in its composition and its world-wide membership. Each issue of Biology and Philosophy carries one or more discussions or comparative reviews, permitting the in-depth study of important works and topics.

  3. 3
    Dionisio says:

    The end of everything is in its beginning, they say. The science that put people on the moon has degenerated to speculation about why ET isn’t returning our calls and how many multiverses can be crammed into a black hole.

    Apparently we got into this current situation after modern science moved away from its humble beginning, when thinking persons of the caliber of Isaac Newton, guided by their theistic worldview, limited their brilliant conclusions to logical, coherent, comprehensive, detailed descriptions of the observed reality that was describable, while humbly keeping off any speculation on issues that were not describable.

    As soon as humans arrogantly decided to describe the unknown in a speculative manner, by adding unproven conjectures, thus mixing science with philosophy, subjective worldview became a growing determinant of the conclusions they arrived to. Really pathetic. Is there a way out of this mess? Is it too late? Yes, no, maybe?

  4. 4
    Querius says:

    Great observations!

    It brings to mind Joseph Lister and the blindness of the “consensus” of the medical community at that time. Some things never change!

    Scientific institutions are as vulnerable to the corruption of prestige, power, bureaucrats, policies, institutions and agencies, reputation, more bureaucrats, jealousies, and money, and bureaucrats as are governmental politics.

    Maybe someone should start a scientific unjournal dedicated to anonymous scientific publication and civil discussion. No money would be involved. Sounds like some internet forums already . . . hmmm.

    -Q

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